Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007359.1 Kokia drynarioides strain JFW-HI SEQ_121975, 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: 8396
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Found at i:1255 original size:216 final size:215
Alignment explanation
Indices: 1--2513 Score: 2620
Period size: 216 Copynumber: 11.6 Consensus size: 215
* * * * *
1 TTGTTTACAAAATGACAAACTATTTTGACCAAATAATGCAATTTCCCATGCATGGAATGTTCGAA
1 TTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTTCGA-GCATGGAATGTTCGAA
* * * * *
66 AAATTGCTCGAAGGAATGGATCGTCTTGAA-ACGTTAAGGAACCAAAGTTATAAAATAACTCTTC
65 AAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTA
* * *
130 AAAGTTTGACTAGTTCGGAAGTTCGTCCAATAACCAAGAGAGAAAGAATTCTCACGTAAATAAGT
130 AAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGT
195 TTTTAATTCAAAGACCAAAAC
195 TTTTAATTCAAAGACCAAAAC
* * * * *
216 TTGTTAACAAAATGACAAACTATTTAGACCAAATGATGTGATTTCCCAAGCATGGAATGTTCAAA
1 TTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTT-TCGAGCATGGAATGTTCGAA
* * * * *
281 AAATTGATCGAAGGAATGGATCATCTTGAATACTTTAAAGAAGCGAAGTTATAAAAGAACTTGTA
65 AAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTA
* *
346 AAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACC---AGAGAAATAATTCTCATGTAAATAAGT
130 AAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGT
* * *
408 TTTTAATTCGATGACAAAAAC
195 TTTTAATTCAAAGACCAAAAC
* * * * *
429 TTGTTCACAAAATGACAAACTATTTAGACCAATTGATGTGATTTTTTGAGCATGAAATGTTCGAA
1 TTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGA-TTTTCGAGCATGGAATGTTCGAA
* ** * ** * * * *
494 AATTTTTTCGAAGGAATGGATCGGCTCAAATACTTTAAGGAATCGAATTTATAAAAGAACTTGAA
65 AAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTA
** * **
559 AAAGTTTGACAAGTTCAAAAGTTTGTCCAAGAACCAAGAGAGAAACAATTCTCATATAAATAAGT
130 AAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGT
624 TTTTAATTCAAAGA-CAAAAC
195 TTTTAATTCAAAGACCAAAAC
* * * * * * * *
644 CTATTTACAAATTGAC--ATTATTTAGGCCAAATGATGCGATTTACTAAGCATGGAATGTTCGGA
1 TTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTTC-GAGCATGGAATGTTCGAA
* * * * * * *
707 AAATTGGTC-AACGGAATGGATCATCTTGTATACTCTCAA-GAACTGAAGTTATAAAAGAATTCA
65 AAATTGCTCGAA-GGAATGGATCGTCTTGAATACT-TTAAGGAACCGAAGTTATAAAAGAACTCG
*
770 TAACAGTTTGACAAGTTC-GATAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATA
128 TAAAAGTTTGACAAGTTCGGA-AGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATA
** *
834 AGTTTTTAACCCAAAGCCCAAAAC
192 AGTTTTTAATTCAAAGACCAAAAC
* * * * * *
858 TTTTTTACAACATAACAAACTATTTAGACCAAATGATGCGACTTTTAGAGAATGGAATGTTTGAA
1 TTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGA-TTTTCGAGCATGGAATGTTCGAA
* * * * *
923 AAATTGATCGAA-GAATGGATTGTCTTGAATATTTTAAGGAACCGAATTTATAAAAGAACTTGTA
65 AAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTA
* * * * * * * *
987 AAAGTTTGACAAGTTTGAAAGTTCTTCCACGAACTAAAAGAGAAACAATTCTCATGTAAAAAAGT
130 AAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGT
* *
1052 TTTTCATTCGAAGACCAAAAC
195 TTTTAATTCAAAGACCAAAAC
* * * *
1073 TTGTTTACAAAATGACAAACTATTTAGA-TAGATTGTTGCGATTTTCGAAGCATGGAATGTTAGA
1 TTGTTTACAAAATGACAAACTATTTAGACCA-AATGATGCGATTTTCG-AGCATGGAATGTTCGA
* * *
1137 AAAATTGCTCGAAGGAATGTATCGCCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGT
64 AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGT
* * *
1202 AAAAGTTTGACAAGTGT-GGAAGTTCATCCATGAACCAAGAGAGAAACAATTCTCACGTAAAGAA
129 AAAAGTTTGACAAGT-TCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAA
1266 GTTTTTAATTCAAAGACCAAAAC
193 GTTTTTAATTCAAAGACCAAAAC
* * * * *
1289 TTGTTTGA-AAAATGACAAATTATTTAGACACTTGTTTGAAA-AATGACAAATTATTTAGACCA-
1 TTGTTT-ACAAAATGACAAACTATTTAGAC-C-------AAATGATG-C-GA-T-TTTCGAGCAT
* * * *
1351 --AATGATGCG---ACTT-CTCGAGCATGGAATGGATTC-TCTTGAATACTTTAACGAACTGAAG
53 GGAATG-TTCGAAAAATTGCTCGA--A-GGAATGGA-TCGTCTTGAATACTTTAAGGAACCGAAG
** * * *
1409 TTATAAAAGAACTCGTAACAA-TTTGATGAGTTTGGATGTTCGTCCAAGAACCAATAGAGAAACA
113 TTATAAAAGAACTCGTAA-AAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACA
* ** *
1473 ATTCTCACGTAAATAAGTATTTAATTCGCAGACAAAAAC
177 ATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAC
* * * * * * *
1512 TTGTTTACAAAATGATAAACTATTTAGACCAAGTGATGCGATTTCCCGAGCATAGATTGTTTGGA
1 TTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTT-TCGAGCATGGAATGTTCGAA
* * * *
1577 AATTTGCTTC-AATGAATGAATCGTCTTGAATTCTTTAAGGAACCGAAGTTATAAAAGAA-TACG
65 AAATTGC-TCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACT-CG
* * * * *
1640 TAAACGCTTGACAAGTTCAGAAGTTCGTCCAAGAACTAAGAGAGAAATAATTCTCACGTAAATAA
128 TAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAA
*
1705 GTTTTTTAATTCACAGACCAAAAC
193 G-TTTTTAATTCAAAGACCAAAAC
* * * *
1729 TTGTTTACAAAACGACAAACTTTTTAGACCAAATGATGCGATTTCTTGAGCATGGAATGCTCGAA
1 TTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTT-TCGAGCATGGAATGTTCGAA
* * * * * *
1794 AAATTACTCGAAAGAATGGATCGTCTTGAATACTTGT-TGGAATCAAAGTAATAAAAGAACTCGT
65 AAATTGCTCGAAGGAATGGATCGTCTTGAATACTT-TAAGGAACCGAAGTTATAAAAGAACTCGT
* * * * * * *
1858 AAAAATTTAACAAGTTCGAAAGTTTGTCAAATAA-CATGGAGAGAAACAATTCTCACGTAAATAA
129 AAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCA-AGAGAGAAACAATTCTCACGTAAATAA
** *
1922 GTTTTTAATTCACTGACAAAAAC
193 GTTTTTAATTCAAAGACCAAAAC
* * * * *
1945 TTGTTTACAAAATGACAAACTATTTTGACAAAATGATGTGATTTCTCGAGAATGGAATGTT-TAG
1 TTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTT-TCGAGCATGGAATGTTCGA-
* * * * *
2009 AAAATTTCTCGAAGGAATGGATCGTCTT-AAAACGTTAAGGAACCAAAGTTATAAAAGAACTCTT
64 AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGT
* * * * * * *
2073 CAAAGTTTGACTAGTTTGGAAGTTCATCTAAGAACCAAGAGAGAAACAATTTTTACGTAAATAAG
129 AAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAG
*
2138 TTTTTAATTCAAAGCCCAAAAC
194 TTTTTAATTCAAAGACCAAAAC
* * **
2160 TTTTTTTACAAAATAACAAACTATTTAGACCAAATGATGCGACTTCCCGAGCATGGAATGTTCGA
1 -TTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGA-TTTTCGAGCATGGAATGTTCGA
* ** * *
2225 AAAATTGCTCGAAGGAATGAATTATCTTGAATACTTTCAGGAATCGAAGTTATAAAAGAACTCGT
64 AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGT
* *
2290 AAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGGGAGAAACAATTCTCATGTAAATAAG
129 AAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAG
* * * *
2355 TTTTTAATTCGATGACAAAAAG
194 TTTTTAATTCAAAGACCAAAAC
* * * * * * *
2377 TTGTTCATAAAATGAAAAATTATTTAGACCAATTGATGCGATTTTCTGATCATGAAATGTTCGAA
1 TTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTTC-GAGCATGGAATGTTCGAA
* * * * * * * * *
2442 AAATTTCTCGAAAGAATGTATCGGCTTAAATGCTTTAAGGAACCGAATTTGTTAAAGAACTCGTA
65 AAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTA
2507 AAAGTTT
130 AAAGTTT
2514 ACTTCCGATC
Statistics
Matches: 1896, Mismatches: 333, Indels: 137
0.80 0.14 0.06
Matches are distributed among these distances:
212 8 0.00
213 333 0.18
214 34 0.02
215 374 0.20
216 676 0.36
217 286 0.15
218 5 0.00
219 2 0.00
220 7 0.00
221 3 0.00
222 4 0.00
223 146 0.08
224 8 0.00
225 2 0.00
226 4 0.00
227 4 0.00
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (215 bp):
TTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTTCGAGCATGGAATGTTCGAAA
AATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAA
AAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT
TTTAATTCAAAGACCAAAAC
Found at i:1322 original size:31 final size:31
Alignment explanation
Indices: 1287--1348 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
1277 AAAGACCAAA
1287 ACTTGTTTGAAAAATGACAAATTATTTAGAC
1 ACTTGTTTGAAAAATGACAAATTATTTAGAC
1318 ACTTGTTTGAAAAATGACAAATTATTTAGAC
1 ACTTGTTTGAAAAATGACAAATTATTTAGAC
1349 CAAATGATGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (31 bp):
ACTTGTTTGAAAAATGACAAATTATTTAGAC
Found at i:2986 original size:216 final size:214
Alignment explanation
Indices: 2514--3100 Score: 786
Period size: 216 Copynumber: 2.7 Consensus size: 214
2504 GTAAAAGTTT
* *
2514 ACTTCCGATCTTGTCAAACTTTTATGAGTTCTTTTATAACTTTGGTTCCTTAAAGTGTTCAAGAT
1 ACTTCCAATCTTGTCAAACTTTTATGAGTTCTTTTATAACTTTAGTTCCTTAAAGTGTTCAAGA-
* * *
2579 G-ATCCATTCCTTCCAGCAATTTTTCGAACAATCCATGCTTGGGAAATAACATCATTTGGTTTAA
65 GAATCCATTCCTT-TAGCAATTTTTCGAACAATCCATGCTCGGGAAATAACATCATTTGGTCTAA
* *
2643 AATGTTTGTCATTTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTAACGTGAGAATTA
129 AA-GTTTGTCA-TTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTAACATGAAAATTA
*
2708 TTTCTCTCTTGGCTCTTGGACTA
192 GTTCTCTCTTGGCTCTTGGACTA
* ** * * * * *
2731 ATTTTTGAA-CTTGTCAAACTGTTACGAGTTCTTTTATAACTTCAGTTCGTTAAAGTATTCAAGA
1 A-CTTCCAATCTTGTCAAACTTTTATGAGTTCTTTTATAACTTTAGTTCCTTAAAGTGTTCAAGA
* ** *
2795 GAATCCATTCCTTTGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTAGGTCTAA
65 GAATCCATTCCTTT-AGCAATTTTTCGAACAATCCATGCTCGGGAAATAACATCATTTGGTCTAA
* * *
2860 ATAGTTTGTTATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACATGAAAATTGG
129 A-AGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTAACATGAAAATTAG
2925 TTCTCTCTT-GCTTCTTGGA-TGA
193 TTCTCTCTTGGC-TCTTGGACT-A
* * *
2947 ACTTCCAATATTGTCAAAGTTTTATGAGTTCTTTTATAACTTTAGTTCCTTAAAGTGTTCAAGAC
1 ACTTCCAATCTTGTCAAACTTTTATGAGTTCTTTTATAACTTTAGTTCCTTAAAGTGTTCAAGAG
* * *
3012 AATCCATTCCTTCTAGCAATTTTTCGAACAATCTATGCTCGGGAAATAACGTCATTTGATCTAAA
66 AATCCATTCCTT-TAGCAATTTTTCGAACAATCCATGCTCGGGAAATAACATCATTTGGTCT-AA
3077 AAGTTTGTCATTTTGTAAACAAGT
129 AAGTTTGTCATTTTGTAAACAAGT
3101 ATTCAAGGCA
Statistics
Matches: 319, Mismatches: 42, Indels: 19
0.84 0.11 0.05
Matches are distributed among these distances:
215 7 0.02
216 191 0.60
217 117 0.37
218 4 0.01
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.41
Consensus pattern (214 bp):
ACTTCCAATCTTGTCAAACTTTTATGAGTTCTTTTATAACTTTAGTTCCTTAAAGTGTTCAAGAG
AATCCATTCCTTTAGCAATTTTTCGAACAATCCATGCTCGGGAAATAACATCATTTGGTCTAAAA
GTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTAACATGAAAATTAGTTC
TCTCTTGGCTCTTGGACTA
Found at i:3173 original size:98 final size:98
Alignment explanation
Indices: 2999--3186 Score: 227
Period size: 98 Copynumber: 1.9 Consensus size: 98
2989 TAGTTCCTTA
* * * ** **
2999 AAGTGTTCAAGACAATCCATTCCTTCTAGCAATTTTTCGAACAATCTATGCTCGGGAAATAACGT
1 AAGTATTCAAGACAATCCATTCCTTCTAGCAATTTTCCGAACAATCCATGCTCGAAAAATAACAA
*
3064 CATTTGATCTAAAAAGTTTGTCATTTTGTAAAC
66 CATCTGATCTAAAAAGTTTGTCATTTTGTAAAC
* * **
3097 AAGTATTCAAGGCAATCCATTCCTT-TGAGCAATTTTCCGAACATTCCATGCTCGAAAAATTGCA
1 AAGTATTCAAGACAATCCATTCCTTCT-AGCAATTTTCCGAACAATCCATGCTCGAAAAATAACA
*
3161 ACAATCTG-TCTAAATAGTTTGTCATT
65 AC-ATCTGATCTAAAAAGTTTGTCATT
3187 CTGTGAACTA
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
97 1 0.01
98 70 0.93
99 4 0.05
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (98 bp):
AAGTATTCAAGACAATCCATTCCTTCTAGCAATTTTCCGAACAATCCATGCTCGAAAAATAACAA
CATCTGATCTAAAAAGTTTGTCATTTTGTAAAC
Found at i:3631 original size:214 final size:214
Alignment explanation
Indices: 3097--4000 Score: 997
Period size: 210 Copynumber: 4.2 Consensus size: 214
3087 TTTTGTAAAC
*** * * * *
3097 AAGTATTCAAGGCAATCCATTCCTTTGAGCAATTTTCCGAACATTCCATGCTCGAAAAATTGCAA
1 AAGTATTCAAGATGATCCATT-CTTCGAGCAATTTTCCGAACATTCCATGCTCGAGAAATCGCAT
* * * ** * *
3162 CAATCT-GTCTAAATAGTTTGTCATTCTGTGAACTAGTTTTGGTCTTTGATTTAGAAACTTATTT
65 C-ATTTGGTCTAAATAGTTTGTCATTTTGTAAAAAAGTTTTGGTCTTTGAATTAAAAACTTATTT
* * * * * *
3226 ACTTGAGAATTGTTTCTCTCTTTGTTCGTGGACGAACTT-TCAAACTTGTAAAACTTTTACAAGT
129 ACGTGAGAAATGTTTCTCTCTTGGTTCTTGGACGAACTTCTGAAA-TTGTCAAACTTTTACAAGT
* *
3290 TCTTTTTTAACTTTGGTTCCTT
193 TCTTTTATAACTTCGGTTCCTT
* ** * * * * *
3312 AACGTATTCAAGAAGATCCATTCTTTTTAGCAATTTTCCGAACATTTCATGCTTGGGAAGTCACA
1 AA-GTATTCAAGATGATCCATTC-TTCGAGCAATTTTCCGAACATTCCATGCTCGAGAAATCGCA
* * *
3377 TCA-TTGGTCTAAATAGTTTGTCATTTTTTAAAAAAGTTTTGGCCTTTGAATTAAAAACTTCTTT
64 TCATTTGGTCTAAATAGTTTGTCATTTTGTAAAAAAGTTTTGGTCTTTGAATTAAAAACTTATTT
* * * *
3441 ATGTGAGAAATGTTTCTCTCTTGGTTCTTGGACGAGCTTTTGAAATT-TCAAACTTTTACGAGTT
129 ACGTGAGAAATGTTTCTCTCTTGGTTCTTGGACGAACTTCTGAAATTGTCAAACTTTTACAAGTT
*
3505 CTTTTAAAACTTCGGTTCCGTT
194 CTTTTATAACTTCGGTTCC-TT
* * ** *
3527 AAGTATTTAAGATTATCCATTCTTCGAGCAATTTTTTGAACATTCCATGCTCGAGAAGTCGCAT-
1 AAGTATTCAAGATGATCCATTCTTCGAGCAATTTTCCGAACATTCCATGCTCGAGAAATCGCATC
* **
3591 ATTTGGTCTAAATAGTTTGTTATTTTGTAAAAAAAGTTTTGGGATTTGAATTAAAAACTTATTCT
66 ATTTGGTCTAAATAGTTTGTCATTTTGT-AAAAAAGTTTTGGTCTTTGAATTAAAAACTTATT-T
* * *
3656 -CGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCTGAACTTGTCAAACTGTTACAAGTT
129 ACGTGAGAAATGTTTCTCTCTTGGTTCTTGGACGAACTTCTGAAATTGTCAAACTTTTACAAGTT
*
3720 CTTTTATAA-TTC-G-T--TA
194 CTTTTATAACTTCGGTTCCTT
* *
3736 AAGTATTCAAGA-GAATCCATTCTTTCGAGCAATTTTCCAAACATTCCATGCTCGGGAAATCGCA
1 AAGTATTCAAGATG-ATCCATTC-TTCGAGCAATTTTCCGAACATTCCATGCTCGAGAAATCGCA
* * *
3800 TCATTAGGTCTAAATAGTTTGTTATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTT
64 TCATTTGGTCTAAATAGTTTGTCATTTTGTAAAAAAGTTTTGGTCTTTGAATTAAAAACTTATTT
* * * ** *
3865 ACGTGA-AAATTGATTCTCTCTTGCTTCTTGGATGAACTTCTGATCTTGTCAAACTTTTACGAGT
129 ACGTGAGAAA-TGTTTCTCTCTTGGTTCTTGGACGAACTTCTGAAATTGTCAAACTTTTACAAGT
*
3929 TCTTTTATAACTTCAGTTCCTT
193 TCTTTTATAACTTCGGTTCCTT
* * * * *
3951 AAAGTGTTCAAGATGATCCAATCCTTCCAGCAATTTTTCGAACAATCCAT
1 -AAGTATTCAAGATGATCC-ATTCTTCGAGCAATTTTCCGAACATTCCAT
4001 TCTTCGACAA
Statistics
Matches: 583, Mismatches: 84, Indels: 43
0.82 0.12 0.06
Matches are distributed among these distances:
209 23 0.04
210 131 0.22
211 30 0.05
212 3 0.01
213 60 0.10
214 124 0.21
215 117 0.20
216 91 0.16
217 4 0.01
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.41
Consensus pattern (214 bp):
AAGTATTCAAGATGATCCATTCTTCGAGCAATTTTCCGAACATTCCATGCTCGAGAAATCGCATC
ATTTGGTCTAAATAGTTTGTCATTTTGTAAAAAAGTTTTGGTCTTTGAATTAAAAACTTATTTAC
GTGAGAAATGTTTCTCTCTTGGTTCTTGGACGAACTTCTGAAATTGTCAAACTTTTACAAGTTCT
TTTATAACTTCGGTTCCTT
Found at i:4096 original size:111 final size:111
Alignment explanation
Indices: 3899--4111 Score: 259
Period size: 111 Copynumber: 1.9 Consensus size: 111
3889 TTCTTGGATG
* * * * * * *
3899 AACTTCTGATCTTGTCAAACTTTTACGAGTTCTTTTATAACTTCAGTTCCTTAAAGTGTTCAAGA
1 AACTTCTGAACTTGCCAAACATTTACGAGTTCTTTTATAACTTCAGTTCCTGAAACTATACAAGA
* * *
3964 TGATCCAATCCTTCCAGCAATTTTTCGAACAATCCATTCTTCGACA
66 CGATCCAATCCTTCCACCAATTTTCCGAACAATCCATTCTTCGACA
* *
4010 AACTTTTGAACTTGCCAAACATTTACGAGTTCTTTTATAACTTC-GATTCCTGAGACTATACAAG
1 AACTTCTGAACTTGCCAAACATTTACGAGTTCTTTTATAACTTCAG-TTCCTGAAACTATACAAG
* * *
4074 ACGATCCATTCCGTT-GACCAATTTTCCGAACATTCCAT
65 ACGATCCAATCC-TTCCACCAATTTTCCGAACAATCCAT
4112 GCTCGGTAAA
Statistics
Matches: 85, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
110 1 0.01
111 82 0.96
112 2 0.02
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (111 bp):
AACTTCTGAACTTGCCAAACATTTACGAGTTCTTTTATAACTTCAGTTCCTGAAACTATACAAGA
CGATCCAATCCTTCCACCAATTTTCCGAACAATCCATTCTTCGACA
Found at i:4430 original size:216 final size:216
Alignment explanation
Indices: 4000--5613 Score: 1705
Period size: 216 Copynumber: 7.5 Consensus size: 216
3990 GAACAATCCA
* * * * * * * *
4000 TTCTTCGACAAACTTTTGAACTTGCCAAACATTTACGAGTTCTTTTAT-AACTTCGATTCCTGAG
1 TTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAAATTTCG-TTCCTTAA
* ** * * * * *
4064 ACTATACAAGACGATCCATTCCGTT-GACCAATTTTCCGAACATTCCATGCTCGGTAAAA-CACA
65 AGTATTTAAGATGATCCATTCC-TTCGAGCAAATTTCTGAACATTCCATGCTCAG-AAAATCACA
* * * *
4127 TCATTTGG----ACTAGTTCGTCATTTTGTAAACAGGTTTTTGTCTTTGAGTTAAAAACTTATTT
128 TCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTTGTCTTTGAATTAAAAACTTATTT
*
4188 ATGCT-AGAATTGTTTCTCTCTTGG
193 ACG-TGAGAATTGTTTCTCTCTTGG
* * *
4212 TTCTTGGATGAACTTTCGAACTTGTCAAACTTTTATGAGTTCTTTTATAAATTTCGTTTCTTAAA
1 TTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAAATTTCGTTCCTTAAA
* * * *
4277 GTATTTAAGACGATCCAATCCTTCGAGCAAATTTCTGAACATTTCATGCTCAGAAAATCGCATCA
66 GTATTTAAGATGATCCATTCCTTCGAGCAAATTTCTGAACATTCCATGCTCAGAAAATCACATC-
* * * *
4342 ATTT-GTCTAAATAGTTTGCCATTTTGTGAACAAGTTTTTGTCATCGAATTAAAAACTTATTTAC
130 ATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTTGTCTTTGAATTAAAAACTTATTTAC
* *
4406 ATGATAATTGTTTCTC-CATTGG
195 GTGAGAATTGTTTCTCTC-TTGG
* *
4428 TTCTTGGACAAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTAT-AACTTCGGTTCCTTAA
1 TTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAAATTTC-GTTCCTTAA
* * * * * * *
4492 AGTATTCAAGATGATCCATTCTTTCGAGC-TATTTTTCGAACATTCCGTGCGC-GAAAAGTCGCA
65 AGTATTTAAGATGATCCATTCCTTCGAGCAAATTTCT-GAACATTCCATGCTCAGAAAA-TCACA
* * * *
4555 TCATTTGGTCTAAATAGTTTTTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACCTGTTT
128 TCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTTGTCTTTGAATTAAAAACTTATTT
4620 ACGTGAGAATTGTTTCTCTCTTGG
193 ACGTGAGAATTGTTTCTCTCTTGG
** * * * *
4644 TTCTTGGTTGAACTTTTGAACTTGTCAAACTTTTACGAGTTCTTTAAT-AATTTCAGTTCCTGAG
1 TTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAAATTTC-GTTCCTTAA
* * * * * ** * *
4708 AGTATATAAGACGATCCATTCCGTCGACCAATTTTCCAAACATTCCATGCTCAGTATATCACATC
65 AGTATTTAAGATGATCCATTCCTTCGAGCAAATTTCTGAACATTCCATGCTCAGAAAATCACATC
* * *
4773 ATTTGGGCTAAATAGTTTGTCATTTTGTAAACAGGTTTTTGTCTTTGAATTAAAAAGTTATTTAC
130 ATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTTGTCTTTGAATTAAAAACTTATTTAC
*
4838 GTGAGAATTGTTTTTCTCTTGG
195 GTGAGAATTGTTTCTCTCTTGG
* * * *
4860 TTCCTGGACGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAAATTTTGTTTCTTAAA
1 TTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAAATTTCGTTCCTTAAA
* * * *
4925 GTATTTAAGATGATCCAATCCTTCGAGC-AATTTTTCGAACATTTCATGCTCAGAAAATCATATC
66 GTATTTAAGATGATCCATTCCTTCGAGCAAATTTCT-GAACATTCCATGCTCAGAAAATCACATC
* * * * *
4989 AATTT-GTCTAAATAATTT-TCCATTTTGTGAACAAGTTTTTATCATCGAATTAAAAACTTATTT
130 -ATTTGGTCTAAATAGTTTGT-CATTTTGTAAACAAGTTTTTGTCTTTGAATTAAAAACTTATTT
* * * *
5052 ACATGAGAATTATTTCTCCCTTGA
193 ACGTGAGAATTGTTTCTCTCTTGG
* * * *
5076 TTCTTGGACGAACTTACAAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAA
1 TTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAAATTTCGTTCCTTAAA
* * * * *
5141 GTATTTAAGATGATCCATTCCTTTGAGCAATTTTCCGAACATTCCATGCTCAGGAAATCGCATCA
66 GTATTTAAGATGATCCATTCCTTCGAGCAAATTTCTGAACATTCCATGCTCAGAAAATCACATCA
* *** * *
5206 TTAGGTCTAAATAGTTTGTTGCTTTGTAAGCAAGTTTTGGTCTTTGAATTAAAAACTTATTTACG
131 TTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTTGTCTTTGAATTAAAAACTTATTTACG
* * * *
5271 TGAAAAATGATTCTCTCTTGC
196 TGAGAATTGTTTCTCTCTTGG
* * *
5292 TTCTTGGATGAACTTTCGATCTTGTCAAACTTTTACGAGTTCTTTTAT-AACTTCGATTCCTTAA
1 TTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAAATTTCG-TTCCTTAA
* * * * * * * *
5356 AGTGTTCAAGATGATCCATTCCTTCTA-CCAATTTTTCGAATATTCCATGCT-AGGGAAATAACA
65 AGTATTTAAGATGATCCATTCCTTCGAGCAAATTTCT-GAACATTCCATGCTCA-GAAAATCACA
* * * *
5419 TCATTTGGTCTAAA-ATGTTTATCA-TTTGTTAAAAAAGTTTTGGTCTTTGAATTATAAACTTAT
128 TCATTTGGTCTAAATA-GTTTGTCATTTTG-TAAACAAGTTTTTGTCTTTGAATTAAAAACTTAT
*
5482 TTACGTGAGAATTGTTTCTCT-TT-A
191 TTACGTGAGAATTGTTTCTCTCTTGG
* * * *
5506 TTCTTGGACGAACTTTTGAACTTGCCAAA-TATTTACGAGTTCTTTTATAACTTTGGTTCC-TAA
1 TTCTTGGACGAACTTTCGAACTTGTCAAACT-TTTACGAGTTCTTTTATAAATTTCGTTCCTTAA
* * * * * * *
5569 GAGTATATAAGAAGATCCATTTCGTCGACCAATTTTCCGAACATT
65 -AGTATTTAAGATGATCCATTCCTTCGAGCAAATTTCTGAACATT
5614 TCATTGATAC
Statistics
Matches: 1163, Mismatches: 206, Indels: 64
0.81 0.14 0.04
Matches are distributed among these distances:
211 6 0.01
212 94 0.08
213 14 0.01
214 72 0.06
215 55 0.05
216 901 0.77
217 21 0.02
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.40
Consensus pattern (216 bp):
TTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAAATTTCGTTCCTTAAA
GTATTTAAGATGATCCATTCCTTCGAGCAAATTTCTGAACATTCCATGCTCAGAAAATCACATCA
TTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTTGTCTTTGAATTAAAAACTTATTTACG
TGAGAATTGTTTCTCTCTTGG
Found at i:4742 original size:755 final size:747
Alignment explanation
Indices: 3276--4742 Score: 1877
Period size: 755 Copynumber: 1.9 Consensus size: 747
3266 CAAACTTGTA
* * * * * * ** *
3276 AAACTTTTACAAGTTCTTTTTTAACTTTGGTTCCTTAACGTATTCAAGAAGATCCATTCTTTTTA
1 AAACATTTACAAGTTCTTTTATAACTTCGATTCCTGAACGTATACAAGAAGATCCATTCCGTTGA
* * * ** * *
3341 GCAATTTTCCGAACATTTCATGCTTGGGAAGTCACATCATTGGTCTAAATAGTTTGTCATTTTTT
66 CCAATTTTCCGAACATTCCATGCTCGGGAAAACACATCATTGG--T-AATAGTTCGTCATTTTGT
*
3406 AAAAAAGTTTTGGCCTTTGAATTAAAAACTTCTTTATGTGAGAAATGTTTCTCTCTTGGTTCTTG
128 AAAAAAGTTTTGGCCTTTGAATTAAAAACTTATTTATGTGAGAAATGTTTCTCTCTTGGTTCTTG
* *
3471 GACGAGCTTTTGAAATTTCAAACTTTTACGAGTTCTTTTAAAACTTCGGTTCCGTTAAGTATTTA
193 GACGAACTTTCGAAATTTCAAACTTTTACGAGTTCTTTTAAAACTTCGGTTCCGTTAAGTATTTA
** * * * *
3536 AGATTATCCATTCTTCGAGCAATTTTTTGAACATTCCATGCTCGAGAAGTCGCATATTTGGTCTA
258 AGACGATCCATCCTTCGAGCAAATTTCTGAACATTCCATGCTCGAGAAATCGCATATTTGGTCTA
** * * *
3601 AATAGTTTGTTATTTTGTAAAAAAAGTTTTGGGATTTGAATTAAAAACTTATTCTCGTGAGAATT
323 AATAGTTTGCCATTTTGTAAAAAAAGTTTTGGCATTCGAATTAAAAACTTATTCTCATGAGAATT
*
3666 GTTTCTCTCTTGGTTCTTGGACGAACTTCTGAACTTGTCAAACTGTTACAAGTTCTTTTATAATT
388 GTTTCTCTCTTGGTTCTTGGACAAACTTCTGAACTTGTCAAACTGTTACAAGTTCTTTTATAATT
* *
3731 CGTTAAAGTATTCAAGAGAATCCATTCTTTCGAGCAATTTTCCAAACATTCCATGCTCGGGAAAT
453 CGTTAAAGTATTCAAGAGAATCCATTCTTTCGAGCAATTTTCCAAACATTCCATGCGCGGAAAAT
*
3796 CGCATCATTAGGTCTAAATAGTTTGTTATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTT
518 CGCATCATTAGGTCTAAATAGTTTGTTATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACCT
*
3861 ATTTACGTGAAAATTGATTCTCTCTTGCTTCTTGGATGAACTTCTGATCTTGTCAAACTTTTACG
583 ATTTACGTGAAAATTGATTCTCTCTTGCTTCTTGGATGAACTTCTGAACTTGTCAAACTTTTACG
* * * * * *
3926 AGTTCTTTTATAACTTCAGTTCCTTAAAGTGTTCAAGATGATCCAATCCTTCCAGCAATTTTTCG
648 AGTTCTTTAATAACTTCAGTTCCTGAAAGTATTCAAGACGATCCAATCCGTCCACCAATTTTTCG
3991 AACAATCCATTCTTCGACAAACTTTTGAACTTGCC
713 AACAATCCATTCTTCGACAAACTTTTGAACTTGCC
* *
4026 AAACATTTACGAGTTCTTTTATAACTTCGATTCCTGAGAC-TATACAAGACGATCCATTCCGTTG
1 AAACATTTACAAGTTCTTTTATAACTTCGATTCCTGA-ACGTATACAAGAAGATCCATTCCGTTG
* *
4090 ACCAATTTTCCGAACATTCCATGCTCGGTAAAACACATCATTTGG-ACTAGTTCGTCATTTTGTA
65 ACCAATTTTCCGAACATTCCATGCTCGGGAAAACACATCA-TTGGTAATAGTTCGTCATTTTGTA
* * * * * *
4154 AACAGGTTTTTGTCTTTGAGTTAAAAACTTATTTATGCT-AGAATTGTTTCTCTCTTGGTTCTTG
129 AAAAAGTTTTGGCCTTTGAATTAAAAACTTATTTATG-TGAGAAATGTTTCTCTCTTGGTTCTTG
* * * * *
4218 GATGAACTTTCGAACTTGTCAAACTTTTATGAGTTCTTTTATAAATTTC-GTTTC-TTAAAGTAT
193 GACGAACTTTCGAAATT-TCAAACTTTTACGAGTTCTTTTA-AAACTTCGGTTCCGTT-AAGTAT
*
4281 TTAAGACGATCCAATCCTTCGAGCAAATTTCTGAACATTTCATGCTC-AGAAAATCGCATCAATT
255 TTAAGACGATCC-ATCCTTCGAGCAAATTTCTGAACATTCCATGCTCGAG-AAATCGCAT--ATT
* * *
4345 T-GTCTAAATAGTTTGCCATTTTGT-GAACAAGTTTTTGTCA-TCGAATTAAAAACTTATT-TAC
316 TGGTCTAAATAGTTTGCCATTTTGTAAAAAAAG-TTTTGGCATTCGAATTAAAAACTTATTCT-C
* * *
4406 ATGATAATTGTTTCTC-CATTGGTTCTTGGACAAACTT-TCGAACTTGTCAAACTTTTACGAGTT
379 ATGAGAATTGTTTCTCTC-TTGGTTCTTGGACAAACTTCT-GAACTTGTCAAACTGTTACAAGTT
* * *
4469 CTTTTATAACTTCGGTTCCTTAAAGTATTCAAGATG-ATCCATTCTTTCGAGCTATTTTTCGAAC
442 CTTTTATAA-TTC-G----TTAAAGTATTCAAGA-GAATCCATTCTTTCGAGCAATTTTCCAAAC
* *
4533 ATTCCGTGCGC-GAAAAGTCGCATCATTTGGTCTAAATAGTTT-TTCATTTTGTAAACAAGTTTT
500 ATTCCATGCGCGGAAAA-TCGCATCATTAGGTCTAAATAGTTTGTT-ATTTTGTAAACAAGTTTT
* * * * * *
4596 GGTCTTTGAATTAAAAACCTGTTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGTTGAACTTTT
563 GGTCTTTGAATTAAAAACCTATTTACGTGAAAATTGATTCTCTCTTGCTTCTTGGATGAACTTCT
* *
4661 GAACTTGTCAAACTTTTACGAGTTCTTTAATAATTTCAGTTCCTGAGAGTATAT-AAGACGATCC
628 GAACTTGTCAAACTTTTACGAGTTCTTTAATAACTTCAGTTCCTGAAAGTAT-TCAAGACGATCC
* *
4725 ATTCCGTCGACCAATTTT
692 AATCCGTCCACCAATTTT
4743 CCAAACATTC
Statistics
Matches: 615, Mismatches: 78, Indels: 43
0.84 0.11 0.06
Matches are distributed among these distances:
747 86 0.14
748 48 0.08
749 130 0.21
750 114 0.19
751 11 0.02
754 6 0.01
755 218 0.35
756 2 0.00
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (747 bp):
AAACATTTACAAGTTCTTTTATAACTTCGATTCCTGAACGTATACAAGAAGATCCATTCCGTTGA
CCAATTTTCCGAACATTCCATGCTCGGGAAAACACATCATTGGTAATAGTTCGTCATTTTGTAAA
AAAGTTTTGGCCTTTGAATTAAAAACTTATTTATGTGAGAAATGTTTCTCTCTTGGTTCTTGGAC
GAACTTTCGAAATTTCAAACTTTTACGAGTTCTTTTAAAACTTCGGTTCCGTTAAGTATTTAAGA
CGATCCATCCTTCGAGCAAATTTCTGAACATTCCATGCTCGAGAAATCGCATATTTGGTCTAAAT
AGTTTGCCATTTTGTAAAAAAAGTTTTGGCATTCGAATTAAAAACTTATTCTCATGAGAATTGTT
TCTCTCTTGGTTCTTGGACAAACTTCTGAACTTGTCAAACTGTTACAAGTTCTTTTATAATTCGT
TAAAGTATTCAAGAGAATCCATTCTTTCGAGCAATTTTCCAAACATTCCATGCGCGGAAAATCGC
ATCATTAGGTCTAAATAGTTTGTTATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACCTATT
TACGTGAAAATTGATTCTCTCTTGCTTCTTGGATGAACTTCTGAACTTGTCAAACTTTTACGAGT
TCTTTAATAACTTCAGTTCCTGAAAGTATTCAAGACGATCCAATCCGTCCACCAATTTTTCGAAC
AATCCATTCTTCGACAAACTTTTGAACTTGCC
Found at i:4813 original size:432 final size:432
Alignment explanation
Indices: 4000--5613 Score: 1900
Period size: 432 Copynumber: 3.8 Consensus size: 432
3990 GAACAATCCA
* * * * * *
4000 TTCTTCGACAAACTTTTGAACTTGCCAAACATTTACGAGTTCTTTTATAACTTCGATTCCTGAGA
1 TTCTTGGACAAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGATTCCTTAAA
* * * * * *
4065 CTATACAAGACGATCCATTCCGTT-GACCAATTTTCCGAACATTCCATGCTCGGTAAAA-CACAT
66 GTATTCAAGATGATCCATTCC-TTCGACCAATTTTTCGAACATTCCATGCGCAG-AAAATCACAT
* ** * * *
4128 CATTTGG----ACTAGTTCGTCATTTTGTAAACAGGTTTTTGTCTTTGAGTTAAAAACTTATTTA
129 CATTTGGTCTAAATAGTTTTTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTA
* * * *
4189 TGCT-AGAATTGTTTCTCTCTTGGTTCTTGGATGAACTTTCGAACTTGTCAAACTTTTATGAGTT
194 CG-TGAGAATTGTTTCTCTCTTGATTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTT
* * * * * * * * *
4253 CTTTTATAAATTTCGTTTCTTAAAGTATTTAAGACGATCCAATCCTTCGAGCAAATTTCTGAACA
258 CTTTTATAACTTTGGTTCCTTAAAGTATATAAGACGATCCATTCCGTCGACCAATTTTCCGAACA
* * *
4318 TTTCATGCTCAGAAAATCGCATCAATTT-GTCTAAATAGTTTGCCATTTTGTGAACAAGTTTTTG
323 TTCCATGCTCAGAAAATCGCATC-ATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTTG
* * * *
4382 TCATCGAATTAAAAACTTATTTACATGATAATTGTTTCTC-CATTGG
387 TCTTTGAATTAAAAACTTATTTACGTGAAAATTGTTTCTCTC-TTGG
*
4428 TTCTTGGACAAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAA
1 TTCTTGGACAAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGATTCCTTAAA
* * * * *
4493 GTATTCAAGATGATCCATTCTTTCGAGCTATTTTTCGAACATTCCGTGCGC-GAAAAGTCGCATC
66 GTATTCAAGATGATCCATTCCTTCGACCAATTTTTCGAACATTCCATGCGCAGAAAA-TCACATC
* *
4557 ATTTGGTCTAAATAGTTTTTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACCTGTTTAC
130 ATTTGGTCTAAATAGTTTTTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTAC
* ** *
4622 GTGAGAATTGTTTCTCTCTTGGTTCTTGGTTGAACTTTTGAACTTGTCAAACTTTTACGAGTTCT
195 GTGAGAATTGTTTCTCTCTTGATTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCT
* * * * *
4687 TTAATAA-TTTCAGTTCCTGAGAGTATATAAGACGATCCATTCCGTCGACCAATTTTCCAAACAT
260 TTTATAACTTT-GGTTCCTTAAAGTATATAAGACGATCCATTCCGTCGACCAATTTTCCGAACAT
* * * * *
4751 TCCATGCTCAGTATATCACATCATTTGGGCTAAATAGTTTGTCATTTTGTAAACAGGTTTTTGTC
324 TCCATGCTCAGAAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTTGTC
* * *
4816 TTTGAATTAAAAAGTTATTTACGTGAGAATTGTTTTTCTCTTGG
389 TTTGAATTAAAAACTTATTTACGTGAAAATTGTTTCTCTCTTGG
* * * * * *
4860 TTCCTGGACGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAAATTTTG-TTTCTTAA
1 TTCTTGGACAAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTAT-AACTTCGATTCCTTAA
* * * * * *
4924 AGTATTTAAGATGATCCAATCCTTCGAGCAATTTTTCGAACATTTCATGCTCAGAAAATCATATC
65 AGTATTCAAGATGATCCATTCCTTCGACCAATTTTTCGAACATTCCATGCGCAGAAAATCACATC
* * * ** * *
4989 AATTT-GTCTAAATAATTTTCCATTTTGTGAACAAGTTTTTATCATCGAATTAAAAACTTATTTA
130 -ATTTGGTCTAAATAGTTTTTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTA
* * * * *
5053 CATGAGAATTATTTCTCCCTTGATTCTTGGACGAACTTACAAACTTGTCAAACTTTTACGAGTTC
194 CGTGAGAATTGTTTCTCTCTTGATTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTC
* * * * *
5118 TTTTATAACTTTGGTTCCTTAAAGTATTTAAGATGATCCATTCCTTTGAGCAATTTTCCGAACAT
259 TTTTATAACTTTGGTTCCTTAAAGTATATAAGACGATCCATTCCGTCGACCAATTTTCCGAACAT
* * *** * *
5183 TCCATGCTCAGGAAATCGCATCATTAGGTCTAAATAGTTTGTTGCTTTGTAAGCAAGTTTTGGTC
324 TCCATGCTCAGAAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTTGTC
* * *
5248 TTTGAATTAAAAACTTATTTACGTGAAAAATGATTCTCTCTTGC
389 TTTGAATTAAAAACTTATTTACGTGAAAATTGTTTCTCTCTTGG
** *
5292 TTCTTGGATGAACTTTCGATCTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGATTCCTTAAA
1 TTCTTGGACAAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGATTCCTTAAA
* * * * * *
5357 GTGTTCAAGATGATCCATTCCTTCTACCAATTTTTCGAATATTCCATGC-TAGGGAAATAACATC
66 GTATTCAAGATGATCCATTCCTTCGACCAATTTTTCGAACATTCCATGCGCA-GAAAATCACATC
* * *
5421 ATTTGGTCTAAA-ATGTTTATCA-TTTGTTAAAAAAGTTTTGGTCTTTGAATTATAAACTTATTT
130 ATTTGGTCTAAATA-GTTTTTCATTTTG-TAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTT
* *
5484 ACGTGAGAATTGTTTCTCT-TT-ATTCTTGGACGAACTTTTGAACTTGCCAAA-TATTTACGAGT
193 ACGTGAGAATTGTTTCTCTCTTGATTCTTGGACGAACTTTCGAACTTGTCAAACT-TTTACGAGT
* *
5546 TCTTTTATAACTTTGGTTCC-TAAGAGTATATAAGAAGATCCATTTCGTCGACCAATTTTCCGAA
257 TCTTTTATAACTTTGGTTCCTTAA-AGTATATAAGACGATCCATTCCGTCGACCAATTTTCCGAA
5610 CATT
321 CATT
5614 TCATTGATAC
Statistics
Matches: 1008, Mismatches: 156, Indels: 42
0.84 0.13 0.03
Matches are distributed among these distances:
426 4 0.00
427 3 0.00
428 108 0.11
429 4 0.00
430 93 0.09
431 25 0.02
432 753 0.75
433 18 0.02
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.40
Consensus pattern (432 bp):
TTCTTGGACAAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGATTCCTTAAA
GTATTCAAGATGATCCATTCCTTCGACCAATTTTTCGAACATTCCATGCGCAGAAAATCACATCA
TTTGGTCTAAATAGTTTTTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACG
TGAGAATTGTTTCTCTCTTGATTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTT
TTATAACTTTGGTTCCTTAAAGTATATAAGACGATCCATTCCGTCGACCAATTTTCCGAACATTC
CATGCTCAGAAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTTGTCTT
TGAATTAAAAACTTATTTACGTGAAAATTGTTTCTCTCTTGG
Found at i:5242 original size:648 final size:647
Alignment explanation
Indices: 4010--5617 Score: 2208
Period size: 648 Copynumber: 2.5 Consensus size: 647
4000 TTCTTCGACA
* * * *
4010 AACTTTTGAACTTGCCAAACATTTACGAGTTCTTTTATAACTTCGATTCCTGAGACTATACAAGA
1 AACTTTTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGATTCCTGAGAGTATATAAGA
* * *
4075 CGATCCATTCCGTTGACCAATTTTCCGAACATTCCATGCTCGGTAAAACACATCATTT-GG---A
66 CGATCCATTCCGTCGACCAATTTTCCGAACATTCCATGCTCAGTAAATCACATCATTTGGGCTAA
* * * *
4136 CTAGTTCGTCATTTTGTAAACAGGTTTTTGTCTTTGAGTTAAAAACTTATTTATGCT-AGAATTG
131 ATAGTTTGTCATTTTGTAAACAGGTTTTTGTCTTTGAATTAAAAACTTATTTACG-TGAGAATTG
* * *
4200 TTTCTCTCTTGGTTCTTGGATGAACTTTCGAACTTGTCAAACTTTTATGAGTTCTTTTATAAATT
195 TTTTTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAAATT
* * *
4265 TCGTTTCTTAAAGTATTTAAGACGATCCAATCCTTCGAGCAA-ATTTCTGAACATTTCATGCTCA
260 TTGTTTCTTAAAGTATTTAAGAAGATCCAATCCTTCGAGCAATTTTTC-GAACATTTCATGCTCA
* * *
4329 GAAAATCGCATCAATTTGTCTAAATAGTTTGCCATTTTGTGAACAAGTTTTTGTCATCGAATTAA
324 GAAAATCACATCAATTTGTCTAAATAATTTGCCATTTTGTGAACAAGTTTTTATCATCGAATTAA
* * * * *
4394 AAACTTATTTACATGATAATTGTTTCTCCATTGGTTCTTGGACAAACTTTCGAACTTGTCAAACT
389 AAACTTATTTACATGAGAATTATTTCTCCATTGATTCTTGGACAAACTTACAAACTTGTCAAACT
*
4459 TTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGATGATCCATTCTTTCGAGCTAT
454 TTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGATGATCCATTCTTTCGAGCAAT
* * *
4524 TTTTCGAACATTCCGTGCGCGAAAAGTCGCATCATTTGGTCTAAATAGTTTTTCATTTTGTAAAC
519 TTTCCGAACATTCCATGCGCGAAAAGTCGCATCATTAGGTCTAAATAGTTTTTCA-TTTGTAAAC
* * * * * *
4589 AAGTTTTGGTCTTTGAATTAAAAACCTGTTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGTTG
583 AAGTTTTGGTCTTTGAATTAAAAACCTATTTACGTGAAAAATGATTCTCTCTTGCTTCTTGGATG
* *
4654 AACTTTTGAACTTGTCAAACTTTTACGAGTTCTTTAATAATTTC-AGTTCCTGAGAGTATATAAG
1 AACTTTTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGA-TTCCTGAGAGTATATAAG
* *
4718 ACGATCCATTCCGTCGACCAATTTTCCAAACATTCCATGCTCAGTATATCACATCATTTGGGCTA
65 ACGATCCATTCCGTCGACCAATTTTCCGAACATTCCATGCTCAGTAAATCACATCATTTGGGCTA
*
4783 AATAGTTTGTCATTTTGTAAACAGGTTTTTGTCTTTGAATTAAAAAGTTATTTACGTGAGAATTG
130 AATAGTTTGTCATTTTGTAAACAGGTTTTTGTCTTTGAATTAAAAACTTATTTACGTGAGAATTG
* *
4848 TTTTTCTCTTGGTTCCTGGACGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAAATT
195 TTTTTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAAATT
*
4913 TTGTTTCTTAAAGTATTTAAGATGATCCAATCCTTCGAGCAATTTTTCGAACATTTCATGCTCAG
260 TTGTTTCTTAAAGTATTTAAGAAGATCCAATCCTTCGAGCAATTTTTCGAACATTTCATGCTCAG
* *
4978 AAAATCATATCAATTTGTCTAAATAATTTTCCATTTTGTGAACAAGTTTTTATCATCGAATTAAA
325 AAAATCACATCAATTTGTCTAAATAATTTGCCATTTTGTGAACAAGTTTTTATCATCGAATTAAA
* *
5043 AACTTATTTACATGAGAATTATTTCTCCCTTGATTCTTGGACGAACTTACAAACTTGTCAAACTT
390 AACTTATTTACATGAGAATTATTTCTCCATTGATTCTTGGACAAACTTACAAACTTGTCAAACTT
* *
5108 TTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTTAAGATGATCCATTCCTTT-GAGCAAT
455 TTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGATGATCCATT-CTTTCGAGCAAT
* *
5172 TTTCCGAACATTCCATGCTCAGGAAA-TCGCATCATTAGGTCTAAATAGTTTGTTGC-TTTGTAA
519 TTTCCGAACATTCCATGCGC-GAAAAGTCGCATCATTAGGTCTAAATAGTTT-TT-CATTTGTAA
* *
5235 GCAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAAAAATGATTCTCTCTTGCTTCTTGGA
581 ACAAGTTTTGGTCTTTGAATTAAAAACCTATTTACGTGAAAAATGATTCTCTCTTGCTTCTTGGA
5300 TG
646 TG
* * * * *
5302 AACTTTCGATCTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGATTCCTTAAAGTGT-TCAAG
1 AACTTTTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGATTCCTGAGAGTATAT-AAG
* * * * * * * *
5366 ATGATCCATTCCTTCTACCAATTTTTCGAATATTCCATGCT-AGGGAAATAACATCATTTGGTCT
65 ACGATCCATTCCGTCGACCAATTTTCCGAACATTCCATGCTCA-GTAAATCACATCATTTGGGCT
* * * * *
5430 AAA-ATGTTTATCA-TTTGTTAAAAAAGTTTTGGTCTTTGAATTATAAACTTATTTACGTGAGAA
129 AAATA-GTTTGTCATTTTG-TAAACAGGTTTTTGTCTTTGAATTAAAAACTTATTTACGTGAGAA
** * *
5493 TTG--TTTCTCTTTATTCTTGGACGAACTTTTGAACTTGCCAAA-TATTTACGAGTTCTTTTAT-
192 TTGTTTTTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACT-TTTACGAGTTCTTTTATA
* * * * * * * * *
5554 AACTTTGGTTCCTAAGAGTATATAAGAAGATCCATTTCGTCGACCAATTTTCCGAACATTTCAT
256 AATTTTGTTTCTTAA-AGTATTTAAGAAGATCCAATCCTTCGAGCAATTTTTCGAACATTTCAT
5618 TGATACGAGT
Statistics
Matches: 855, Mismatches: 91, Indels: 34
0.87 0.09 0.03
Matches are distributed among these distances:
643 1 0.00
644 110 0.13
645 15 0.02
646 91 0.11
647 8 0.01
648 614 0.72
649 15 0.02
650 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.40
Consensus pattern (647 bp):
AACTTTTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGATTCCTGAGAGTATATAAGA
CGATCCATTCCGTCGACCAATTTTCCGAACATTCCATGCTCAGTAAATCACATCATTTGGGCTAA
ATAGTTTGTCATTTTGTAAACAGGTTTTTGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGT
TTTTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAAATTT
TGTTTCTTAAAGTATTTAAGAAGATCCAATCCTTCGAGCAATTTTTCGAACATTTCATGCTCAGA
AAATCACATCAATTTGTCTAAATAATTTGCCATTTTGTGAACAAGTTTTTATCATCGAATTAAAA
ACTTATTTACATGAGAATTATTTCTCCATTGATTCTTGGACAAACTTACAAACTTGTCAAACTTT
TACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGATGATCCATTCTTTCGAGCAATTT
TCCGAACATTCCATGCGCGAAAAGTCGCATCATTAGGTCTAAATAGTTTTTCATTTGTAAACAAG
TTTTGGTCTTTGAATTAAAAACCTATTTACGTGAAAAATGATTCTCTCTTGCTTCTTGGATG
Found at i:6359 original size:17 final size:18
Alignment explanation
Indices: 6337--6370 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
6327 ACTTCTTGTT
*
6337 TAGTTTAGTT-AGAGTTC
1 TAGTTTAATTAAGAGTTC
6354 TAGTTTAATTAAGAGTT
1 TAGTTTAATTAAGAGTT
6371 TTATTTAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.29, C:0.03, G:0.21, T:0.47
Consensus pattern (18 bp):
TAGTTTAATTAAGAGTTC
Done.