Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016169.1 Corchorus olitorius cultivar O-4 contig16202, 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: 24859
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:5066 original size:19 final size:20
Alignment explanation
Indices: 5025--5066 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
5015 TGATTAAATG
*
5025 AACTCTAGAAAGTGTATTCA
1 AACTCTAGAAACTGTATTCA
5045 AACTCT-GAAACTCGTATT-A
1 AACTCTAGAAACT-GTATTCA
5064 AAC
1 AAC
5067 CCTATAAGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (20 bp):
AACTCTAGAAACTGTATTCA
Found at i:5421 original size:13 final size:12
Alignment explanation
Indices: 5403--5447 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 12
5393 ATTTTATTAC
5403 TGTTTTATTAAAT
1 TGTTTTA-TAAAT
5416 TGTTTTATAAAT
1 TGTTTTATAAAT
*
5428 GGTTTTAAATAAAT
1 TGTTTT--ATAAAT
5442 TGTTTT
1 TGTTTT
5448 GGGTGCATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 10 0.36
13 7 0.25
14 11 0.39
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (12 bp):
TGTTTTATAAAT
Found at i:6584 original size:72 final size:72
Alignment explanation
Indices: 6462--7400 Score: 967
Period size: 72 Copynumber: 13.0 Consensus size: 72
6452 TGGGTAAGAA
*
6462 CAAGCAAAGACTTAATTTCAAGGAAATGAGGTAAGAA-CAAGCACAA-ACTTAATTCAGGGTAAT
1 CAAGCAAAGACTTAATTTCAAGGAAATTAGGTAA-AATCAAGCA-AAGACTTAATTCAGGGTAAT
*
6525 TAAATAAAT
64 TAAGTAAAT
* * *
6534 C-AGTCAAAGACTTAATTTCAAGGAAATTAGTTAAAATCAAGCAGAGACTTAATTTAGGGTAATT
1 CAAG-CAAAGACTTAATTTCAAGGAAATTAGGTAAAATCAAGCAAAGACTTAATTCAGGGTAATT
6598 AAGTAAAT
65 AAGTAAAT
* * * * *
6606 C-AGTCAAAGACTTAATTTAAAGAAAATTAGGTAAAATTAAGCACAGACTTAATTCAAGGTAATT
1 CAAG-CAAAGACTTAATTTCAAGGAAATTAGGTAAAATCAAGCAAAGACTTAATTCAGGGTAATT
6670 AAGTAAAT
65 AAGTAAAT
* * *
6678 CAAGCAAAGACTTAATTTCAAGGAAATTGGGTAAGAA-CAAGCAAAGACTTAATTTCAAGGAAAT
1 CAAGCAAAGACTTAATTTCAAGGAAATTAGGTAA-AATCAAGCAAAGACTTAA-TTCAGGGTAAT
* *
6742 TAGGTAAGAA
64 TAAGTAA-AT
* * ** * * * *
6752 CAAGCACATACTTAA-TTCGGGGTAATTAAGT-AAATCAAGCAAAGACTTAATTTCAAGGAAATT
1 CAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAAATCAAGCAAAGACTTAA-TTCAGGGTAATT
** *
6815 GGGTAAGAA
65 AAGTAA-AT
* *
6824 CAAACAAAGACTTAATTTCAAGGAAATTAGGTAAGAA-CAAGCACAA-ACTTAATTCGGGGTAAT
1 CAAGCAAAGACTTAATTTCAAGGAAATTAGGTAA-AATCAAGCA-AAGACTTAATTCAGGGTAAT
6887 TAAGTAAAT
64 TAAGTAAAT
* * * * * *
6896 TAAGCAAAGACTTAATTTTAAGGAAATTGGGTAAGAA-CAAACAAAGACTTAATTTCAAGGAAAT
1 CAAGCAAAGACTTAATTTCAAGGAAATTAGGTAA-AATCAAGCAAAGACTTAA-TTCAGGGTAAT
*
6960 TAGGTAAAAT
64 TAAGT-AAAT
* * * * * * *
6970 CAAGCACATACTTAA-TTCAGGGTAATTAAGT-AAATCAAGCAAAGACTTAATTTCAAGGAAATT
1 CAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAAATCAAGCAAAGACTTAA-TTCAGGGTAATT
** *
7033 GGGTAAGAA
65 AAGTAA-AT
* * * *
7042 CAAGCAAAGATTTAATTTCAAGGAAATTAGGTCAAATCAAGCACATACTTAATTCAGGGTAATTA
1 CAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAAATCAAGCAAAGACTTAATTCAGGGTAATTA
7107 AGTAAAT
66 AGTAAAT
** *
7114 CAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAGAA-CAAGCAAAGACTTAATTTCAACGAAAT
1 CAAGCAAAGACTTAATTTCAAGGAAATTAGGTAA-AATCAAGCAAAGACTTAA-TTCAGGGTAAT
* *
7178 TAGGTAAGAA
64 TAAGTAA-AT
*
7188 CAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAAATCAAGCATAGACTTAATTCAGGGTAATTA
1 CAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAAATCAAGCAAAGACTTAATTCAGGGTAATTA
7253 AGTAAAT
66 AGTAAAT
* * *
7260 CAAGCAAAGACTTAATTTCAAGGAAATTAAGT-AAATTAA-CAAAGACTTGATTCAGGGTAATTA
1 CAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAAATCAAGCAAAGACTTAATTCAGGGTAATTA
*
7323 AGTAAAAG
66 AGT-AAAT
* * * * * * * *
7331 CAAACAAAAACTTAA-TTCAGGGTAATTAAGTAAAAGC-AGTCAAGGATTTAATTCAGGGTAATT
1 CAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAAATCAAG-CAAAGACTTAATTCAGGGTAATT
7394 AAGTAAA
65 AAGTAAA
7401 GAGTCAATAA
Statistics
Matches: 737, Mismatches: 103, Indels: 55
0.82 0.12 0.06
Matches are distributed among these distances:
70 40 0.05
71 41 0.06
72 405 0.55
73 138 0.19
74 109 0.15
75 4 0.01
ACGTcount: A:0.47, C:0.11, G:0.17, T:0.25
Consensus pattern (72 bp):
CAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAAATCAAGCAAAGACTTAATTCAGGGTAATTA
AGTAAAT
Found at i:6654 original size:109 final size:109
Alignment explanation
Indices: 6462--7347 Score: 1109
Period size: 109 Copynumber: 8.2 Consensus size: 109
6452 TGGGTAAGAA
* * *
6462 CAAGCAAAGACTTAATTTCAAGGAAATGAGGTAAGAACAAGCACAA-ACTTAA-TTCAGGGTAAT
1 CAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAGAACAAGCA-AAGACTTAATTTCAAGGAAAT
** * * *
6525 TAAAT-AAATC-AGTCAAAGACTTAATTTCAAGGAAATT-AGTTAAAAT
65 TAGGTAAAATCAAG-CACAGACTTAA-TTCAGGGTAATTAAG-T-AAAT
* * * * * * *
6571 CAAGCAGAGACTTAATTT-AGGGTAATTAAGTAA-ATC-AGTCAAAGACTTAATTTAAAGAAAAT
1 CAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAGAACAAG-CAAAGACTTAATTTCAAGGAAAT
* *
6633 TAGGTAAAATTAAGCACAGACTTAATTCAAGGTAATTAAGTAAAT
65 TAGGTAAAATCAAGCACAGACTTAATTCAGGGTAATTAAGTAAAT
*
6678 CAAGCAAAGACTTAATTTCAAGGAAATTGGGTAAGAACAAGCAAAGACTTAATTTCAAGGAAATT
1 CAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAGAACAAGCAAAGACTTAATTTCAAGGAAATT
* *
6743 AGGTAAGAA-CAAGCACATACTTAATTCGGGGTAATTAAGTAAAT
66 AGGTAA-AATCAAGCACAGACTTAATTCAGGGTAATTAAGTAAAT
* *
6787 CAAGCAAAGACTTAATTTCAAGGAAATTGGGTAAGAACAAACAAAGACTTAATTTCAAGGAAATT
1 CAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAGAACAAGCAAAGACTTAATTTCAAGGAAATT
* *
6852 AGGTAAGAA-CAAGCACAAACTTAATTCGGGGTAATTAAGTAAAT
66 AGGTAA-AATCAAGCACAGACTTAATTCAGGGTAATTAAGTAAAT
* * * *
6896 TAAGCAAAGACTTAATTTTAAGGAAATTGGGTAAGAACAAACAAAGACTTAATTTCAAGGAAATT
1 CAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAGAACAAGCAAAGACTTAATTTCAAGGAAATT
*
6961 AGGTAAAATCAAGCACATACTTAATTCAGGGTAATTAAGTAAAT
66 AGGTAAAATCAAGCACAGACTTAATTCAGGGTAATTAAGTAAAT
* *
7005 CAAGCAAAGACTTAATTTCAAGGAAATTGGGTAAGAACAAGCAAAGATTTAATTTCAAGGAAATT
1 CAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAGAACAAGCAAAGACTTAATTTCAAGGAAATT
* *
7070 AGGTCAAATCAAGCACATACTTAATTCAGGGTAATTAAGTAAAT
66 AGGTAAAATCAAGCACAGACTTAATTCAGGGTAATTAAGTAAAT
*
7114 CAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAGAACAAGCAAAGACTTAATTTCAACGAAATT
1 CAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAGAACAAGCAAAGACTTAATTTCAAGGAAATT
* * * *
7179 AGGTAAGAA-CAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAAAT
66 AGGTAA-AATCAAGCACAGACTTAA-TTCAGGGTAATTAAGT-AAAT
* * * * *
7225 CAAGCATAGACTTAA-TTCAGGGTAATTAAGTAA-ATCAAGCAAAGACTTAATTTCAAGGAAATT
1 CAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAGAACAAGCAAAGACTTAATTTCAAGGAAATT
* * * * *
7288 AAGT-AAATTAA-CAAAGACTTGATTCAGGGTAATTAAGTAAAAG
66 AGGTAAAATCAAGCACAGACTTAATTCAGGGTAATTAAGT-AAAT
* *
7331 CAAACAAAAACTTAATT
1 CAAGCAAAGACTTAATT
7348 CAGGGTAATT
Statistics
Matches: 698, Mismatches: 63, Indels: 34
0.88 0.08 0.04
Matches are distributed among these distances:
106 33 0.05
107 44 0.06
108 49 0.07
109 518 0.74
110 36 0.05
111 18 0.03
ACGTcount: A:0.47, C:0.11, G:0.17, T:0.25
Consensus pattern (109 bp):
CAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAGAACAAGCAAAGACTTAATTTCAAGGAAATT
AGGTAAAATCAAGCACAGACTTAATTCAGGGTAATTAAGTAAAT
Found at i:7438 original size:33 final size:34
Alignment explanation
Indices: 7234--7501 Score: 212
Period size: 36 Copynumber: 7.6 Consensus size: 34
7224 TCAAGCATAG
*
7234 ACTTAATTCAGGGTAATTAAGTAA-A-TCAAGCAAA
1 ACTTAATTCAGGGTAATTAAGTAAGAGTCAA--TAA
* * * *
7268 GACTTAATTTCAAGGAAATTAAGTAA-ATTAACAA-AG
1 -ACTTAA-TTCAGGGTAATTAAGTAAGAGT--CAATAA
* * *
7304 ACTTGATTCAGGGTAATTAAGTAAAAG-CAAACAAAA
1 ACTTAATTCAGGGTAATTAAGTAAGAGTC--A-ATAA
**
7340 ACTTAATTCAGGGTAATTAAGTAAAAGCAGTCAA-GG
1 ACTTAATTCAGGGTAATTAAGT--AAG-AGTCAATAA
*
7376 ATTTAATTCAGGGTAATTAAGTAAAGAGTCAATAA
1 ACTTAATTCAGGGTAATTAAGT-AAGAGTCAATAA
*
7411 ACTTAATTCTGGGTAATTAAGT-AGAGTCAATAA
1 ACTTAATTCAGGGTAATTAAGTAAGAGTCAATAA
7444 ACTTAATTC-GAGGTAATTAAGTAA-AGTCAATAAAGA
1 ACTTAATTCAG-GGTAATTAAGTAAGAGTCAAT--A-A
7480 ACTTAATTCAGGGTAATTAAGT
1 ACTTAATTCAGGGTAATTAAGT
7502 GGGGACATTA
Statistics
Matches: 196, Mismatches: 17, Indels: 39
0.78 0.07 0.15
Matches are distributed among these distances:
32 2 0.01
33 38 0.19
34 24 0.12
35 38 0.19
36 82 0.42
37 3 0.02
38 3 0.02
39 5 0.03
40 1 0.01
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.28
Consensus pattern (34 bp):
ACTTAATTCAGGGTAATTAAGTAAGAGTCAATAA
Found at i:8514 original size:22 final size:22
Alignment explanation
Indices: 8486--8536 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
8476 CTTTACCACT
8486 AATTGGACACGTATTAAAGGTA
1 AATTGGACACGTATTAAAGGTA
8508 AATTGGACACGTATTAAAGGTA
1 AATTGGACACGTATTAAAGGTA
8530 AATTGGA
1 AATTGGA
8537 GTGTTGAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.41, C:0.08, G:0.24, T:0.27
Consensus pattern (22 bp):
AATTGGACACGTATTAAAGGTA
Found at i:11130 original size:3 final size:3
Alignment explanation
Indices: 11115--11204 Score: 110
Period size: 3 Copynumber: 30.0 Consensus size: 3
11105 GACCGTCACT
* * *
11115 ATC ATC ATG ATC ATC ATC ATC ATT ATC ATC ATC ATC ATC ATT ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * *
11163 ATC ATT ATC ATC ATC ATC ATC AGC A-C GATT ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC -ATC ATC ATC ATC ATC
11205 TTCTGTAATA
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
2 1 0.01
3 73 0.99
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:11456 original size:2 final size:2
Alignment explanation
Indices: 11445--11479 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
11435 ATAATACTAT
11445 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11480 ATAAAAGAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:18180 original size:334 final size:329
Alignment explanation
Indices: 17129--18939 Score: 1855
Period size: 334 Copynumber: 5.5 Consensus size: 329
17119 CTCTTACACT
* * * * * * * *
17129 CATCACAGTTTTTGG-TTAAACCGTGTTACGGGGCCTCGACTCAGTTTTGTATGCTTTTTGGCAC
1 CATCACGGTTTTTGGCTAAAACCGCGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAC
*
17193 CAAGA-TCCTTGAAATATCTATATTCATCTATTCAATTCTCAGCCACATTGGATTTAAGAATTTG
66 CAAGACTCCTTGAAATATCTATATTCATCTATTCAAATCTCAGCCACATTGGATTTAAGAATTTG
* * * * * *
17257 TTTTAACAAGCATCGGATTCATGTTTCGATTTAATCAGAAATTAATTTGGACAACAATAGGAAAA
131 TTTTTACGAGCATCTGAATCATGTTTCGATTTAATCAAAAATTAATTTGGAAAACAATAGGAAAA
* ** *
17322 ATGATATTAGAATAGTGAAAATCCCTTC-AATTTTTCT--CGTTGAATTATATATTTTTTATTAG
196 ACGATATTAGAAGCGTGAAAATCCCTTCAAATTTTT-TGGCGTTGAATTATATATTTTTTATGAG
* * *
17384 TATTGTGGCCAAAAATTAAAGAAAAATTTATCGGGTCAATTTTTTGCAAAA-TTT--C----AGC
260 TATTGTGGCC-AAAATTGAAGAAAAATTTTTCGGGTCAA-TTTTTGCAAAATTTTAGCTGAAATC
17442 -TG--AA
323 GTGATAA
* * * * *
17446 -ATCACGGTTTTTGGCTAAAATCGCATTCC-GGGTCCCAGCTCAATTTTGCATGATTTATT-GCA
1 CATCACGGTTTTTGGCTAAAACCGCGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTT-TTGGCA
* * * * * * *
17508 CAAAGACTCTTTGAGGAAAATCTATATTCATCTAGTCGAATCTCAGCCATATTGGATTTGAGAAT
65 CCAAGACTCCTTGA--AATATCTATATTCATCTATTCAAATCTCAGCCACATTGGATTTAAGAAT
* * * * * * ** * * **
17573 TCGTTTTTATGAGCACCTGAATCTTGTTTCG-GTTAA-CTAAAAATTAAATTAAAAAAAAAGAAA
128 TTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATC-AAAAATTAATTTGGAAAACAATAGG
* * * * * * * *
17636 AAAAAAGATATTAGAAGCATGACAAGCCCTCCAATTTTTTTTTGCTTTGAATTATATA-TTTTTA
192 AAAAACGATATTAGAAGCGTGAAAATCCCTTCAA-ATTTTTTGGCGTTGAATTATATATTTTTTA
* * * * ** * * * * *
17700 TGACTATTTTGGCAAAAAATTGAGGAATTA-TTTTCAGGTTAATTTTCGGAAAATTTTAGCCGAA
256 TGAGTATTGTGGC-CAAAATTGAAGAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGCTGAA
*
17764 ATCGTG-TAC
320 ATCGTGATAA
*** ** * * * *
17773 CATCACAAATTTTGGCTAAAAATGCGTTACGAGGCCCCGACTCAGTTTTGCATGATTTTTGACAC
1 CATCACGGTTTTTGGCTAAAACCGCGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAC
* * * * * * *
17838 CGAGACTCCTTGAAATATCTATATTTATCTAATCAAATCTCAACCACATTGAAATTAAGGATTTG
66 CAAGACTCCTTGAAATATCTATATTCATCTATTCAAATCTCAGCCACATTGGATTTAAGAATTTG
* * * * *
17903 TTTTTACGAGCATCTAAATCATGTTTCGAATTAATGAGAAATTAATTTTGAAAACAATAGGAAAA
131 TTTTTACGAGCATCTGAATCATGTTTCGATTTAATCAAAAATTAATTTGGAAAACAATAGGAAAA
* * * * * *
17968 ACGATTTTAGAAGCGTGAAAAGCCCTTCAAATGTTTTGGCATTGAATTATATAATTCTTATGAGT
196 ACGATATTAGAAGCGTGAAAATCCCTTCAAATTTTTTGGCGTTGAATTATATATTTTTTATGAGT
* * * *
18033 ATTGTGGACCAAAATTGAGGAAATATTTTTCGGGTCAATCTTTACAAAATTTTAGCTGAAATCGT
261 ATTGTGG-CCAAAATTGAAGAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGCTGAAATCGT
18098 GAACTAA
325 G-A-TAA
*
18105 TCATCACGGTTTTTTTGCTAAAACCGCGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGC
1 -CATCACGG-TTTTTGGCTAAAACCGCGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGC
* * *
18170 ACCAAGACTCCTTGAAATATCTATATTCATCTAGTCAAATCTCAGCCACATTAGATTAAAGAATT
64 ACCAAGACTCCTTGAAATATCTATATTCATCTATTCAAATCTCAGCCACATTGGATTTAAGAATT
* * *
18235 TGTTTTTACAAGCATCTGAATCATGTTTCGATTTAATCAAAAATTAATTTGGAGAACAATACGAA
129 TGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATCAAAAATTAATTTGGAAAACAATAGGAA
* * * * * *
18300 AAACAATATTAGAAGCGTGAAAATCGCTTCAAATTTTTTTGGTGTTAAATTATACATTTTTTATA
194 AAACGATATTAGAAGCGTGAAAATCCCTTCAAA-TTTTTTGGCGTTGAATTATATATTTTTTATG
** * * * ** *
18365 AGTATTGTGGACCAAAA-AAAATAAAAAATTTTCAGGTCTGTTTTTGCAAAGTTTTAGCTGAAAT
258 AGTATTGTGG-CCAAAATTGAAGAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGCTGAAAT
*
18429 CATGTACGTTAA
322 C--GT--GATAA
* *
18441 -ATCACGGTTTTTGGCTAAAACCGCGTTCCGGGGCCGCGGCTCAGTTTTGCATGATTTCTGGCAC
1 CATCACGGTTTTTGGCTAAAACCGCGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAC
* *
18505 CAAGACTCCTTGAAATATCTATATTCATCTATTCAAATCTTAGCCACATTGGATTTAAGGATTTG
66 CAAGACTCCTTGAAATATCTATATTCATCTATTCAAATCTCAGCCACATTGGATTTAAGAATTTG
* * *
18570 TTTTTACGAGCATCTGAATCATTTTTCCATTTAATCAAAAATTAATTTGGACAACAATAGGAAAA
131 TTTTTACGAGCATCTGAATCATGTTTCGATTTAATCAAAAATTAATTTGGAAAACAATAGGAAAA
* * * *
18635 ACGATATTAGAAGCGCGAAAATCCCTTC-AATTTTTTGGCGTTGTATTATGTATTTTTTATTAGT
196 ACGATATTAGAAGCGTGAAAATCCCTTCAAATTTTTTGGCGTTGAATTATATATTTTTTATGAGT
*
18699 ATTGTGGCCAAAAATTGAAGAAAAATATTTT-GGGTCCATTTTTTGC-AAATTTTAGCTGAAATC
261 ATTGTGGCC-AAAATTGAAGAAAAAT-TTTTCGGGT-CAATTTTTGCAAAATTTTAGCTGAAATC
18762 GTGTAATAA
323 GTG--ATAA
** * * * * *
18771 CCATCACAACTTTTT-GCTAAAAACGCGTTCCGGGACCCCGGCTCAATTTTGCTTGCTTTATT-G
1 -CATCAC-GGTTTTTGGCTAAAACCGCGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTT-TTGG
* * * * *
18834 CACCAAAACTCCTTGAATTATCTATAGTCATCTATTCAAGTCTCAGCCACATTGGATTTAAGGAT
63 CACCAAGACTCCTTGAAATATCTATATTCATCTATTCAAATCTCAGCCACATTGGATTTAAGAAT
* *
18899 TTGTTTTTACGAGCATTTGAATCATTTTTCGATTTAATCAA
128 TTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATCAA
18940 TGTTAGGGGT
Statistics
Matches: 1221, Mismatches: 225, Indels: 81
0.80 0.15 0.05
Matches are distributed among these distances:
316 41 0.03
317 18 0.01
318 54 0.04
319 80 0.07
320 32 0.03
321 14 0.01
325 2 0.00
326 2 0.00
327 85 0.07
328 104 0.09
329 69 0.06
330 7 0.01
331 39 0.03
332 173 0.14
333 223 0.18
334 232 0.19
335 40 0.03
336 5 0.00
338 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (329 bp):
CATCACGGTTTTTGGCTAAAACCGCGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAC
CAAGACTCCTTGAAATATCTATATTCATCTATTCAAATCTCAGCCACATTGGATTTAAGAATTTG
TTTTTACGAGCATCTGAATCATGTTTCGATTTAATCAAAAATTAATTTGGAAAACAATAGGAAAA
ACGATATTAGAAGCGTGAAAATCCCTTCAAATTTTTTGGCGTTGAATTATATATTTTTTATGAGT
ATTGTGGCCAAAATTGAAGAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGCTGAAATCGTG
ATAA
Found at i:19182 original size:43 final size:42
Alignment explanation
Indices: 19121--19408 Score: 436
Period size: 43 Copynumber: 6.8 Consensus size: 42
19111 CCAATAACTA
19121 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCC
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATT-C
* *
19164 AAAGTCCTCAAACACATATATAACACAGAGGCATCTCTA-TC
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTC
*
19205 AAAGTCCCCAAACACATATATAACACACGGGCATCTCTATATC
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTAT-TC
* * *
19248 AAAGTCCTCAAACACATATATAACACAGAGGCATCTATA-TC
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTC
* *
19289 AAAGTCCCCAAACACATATATAACACATGAGCATCTCTATATC
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTAT-TC
19332 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATT-C
* *
19375 AAAGTCCTCAAACACATATATAACACAGAGGCAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAT
19409 TTCTCCTTAT
Statistics
Matches: 222, Mismatches: 18, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
41 73 0.33
42 2 0.01
43 147 0.66
ACGTcount: A:0.41, C:0.27, G:0.10, T:0.21
Consensus pattern (42 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTC
Found at i:19220 original size:84 final size:84
Alignment explanation
Indices: 19121--19408 Score: 470
Period size: 84 Copynumber: 3.4 Consensus size: 84
19111 CCAATAACTA
19121 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTAT-TCCAAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATAT-CAAAGTCCTCAAACACATATAT
19185 AACACAGAGGCATCTCTATC
65 AACACAGAGGCATCTCTATC
*
19205 AAAGTCCCCAAACACATATATAACACACGGGCATCTCTATATCAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATATCAAAGTCCTCAAACACATATATA
*
19270 ACACAGAGGCATCTATATC
66 ACACAGAGGCATCTCTATC
* * *
19289 AAAGTCCCCAAACACATATATAACACATGAGCATCTCTATATCAAAGTCCCCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATATCAAAGTCCTCAAACACATATATA
*
19354 ACACAGGGGCATCTCTATTAC
66 ACACAGAGGCATCTCTA-T-C
* *
19375 AAAGTCCTCAAACACATATATAACACAGAGGCAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAT
19409 TTCTCCTTAT
Statistics
Matches: 190, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
84 157 0.83
85 2 0.01
86 31 0.16
ACGTcount: A:0.41, C:0.27, G:0.10, T:0.21
Consensus pattern (84 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATATCAAAGTCCTCAAACACATATATA
ACACAGAGGCATCTCTATC
Found at i:19281 original size:127 final size:126
Alignment explanation
Indices: 19121--19408 Score: 465
Period size: 127 Copynumber: 2.3 Consensus size: 126
19111 CCAATAACTA
* * * *
19121 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCCAAAGTCCTCAAACACATATATA
1 AAAGTCCTCAAACACATATATAACACAGAGGCATCTATA-T-CAAAGTCCCCAAACACATATATA
19186 ACACA-GAGGCATCTC-TATCAAAGTCCCCAAACACATATATAACACACGGGCATCTCTA-TATC
64 ACACATGA-GCATCTCATATCAAAGTCCCCAAACACATATATAACACACGGGCATCTCTATTA-C
19248 AAAGTCCTCAAACACATATATAACACAGAGGCATCTATATCAAAGTCCCCAAACACATATATAAC
1 AAAGTCCTCAAACACATATATAACACAGAGGCATCTATATCAAAGTCCCCAAACACATATATAAC
*
19313 ACATGAGCATCTCTATATCAAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
66 ACATGAGCATCTC-ATATCAAAGTCCCCAAACACATATATAACACACGGGCATCTCTATTAC
19375 AAAGTCCTCAAACACATATATAACACAGAGGCAT
1 AAAGTCCTCAAACACATATATAACACAGAGGCAT
19409 TTCTCCTTAT
Statistics
Matches: 152, Mismatches: 5, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
125 34 0.22
126 3 0.02
127 113 0.74
128 2 0.01
ACGTcount: A:0.41, C:0.27, G:0.10, T:0.21
Consensus pattern (126 bp):
AAAGTCCTCAAACACATATATAACACAGAGGCATCTATATCAAAGTCCCCAAACACATATATAAC
ACATGAGCATCTCATATCAAAGTCCCCAAACACATATATAACACACGGGCATCTCTATTAC
Found at i:19534 original size:2 final size:2
Alignment explanation
Indices: 19527--19553 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19517 TTCCTATCTC
19527 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
19554 CACACATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19562 original size:14 final size:14
Alignment explanation
Indices: 19531--19573 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
19521 TATCTCATAT
* * *
19531 ATATATATATATAT
1 ATATATATACACAC
19545 ATATATATACACAC
1 ATATATATACACAC
*
19559 ATATACATACACAC
1 ATATATATACACAC
19573 A
1 A
19574 CACACACACA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (14 bp):
ATATATATACACAC
Found at i:21578 original size:332 final size:330
Alignment explanation
Indices: 20924--23716 Score: 2509
Period size: 332 Copynumber: 8.5 Consensus size: 330
20914 TCCCACAATC
* * * * *
20924 AGAAATTAATTTGGACAAAAATAGGAAAAACAATATTAGAAGTGCGAAAATAC-CTTCAGT-TTT
1 AGAAATTAATTT-GA-AAAAATAGGAAAAACAATATTAGAAGCGTGAAAA-GCTTTTCAATCTTT
* * ** * * *
20987 TTGGCGTTGAATTCTATATTTTTTATTAGTATTGTGGCCAAAAGCTGAAGAAAAATTTTTTGAGT
63 TTGGCGTTGAATTATATATTTTTTATGAGTATTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGT
** * * * * * * *
21052 CAAATTTTGCAAAAGTTTAGATGAAATCGTGTAATAACCATTACAGTTTTTGGCTAAAAATGTGT
128 CAGTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACCATCACAATTTTTGGCTAAAACTGCGT
* * * * * *
21117 TCCGGGGCCTCAGCTCAATTTTGTATGATTTATT-GTACCAAGACTCCTTGAGATATCTATATTC
193 TCCAGGGCC-CGGCTCAGTTTTGCATGATTT-TTGGCACCAAGACTCCTTGAAATATCTATATTC
* * * * * *
21181 ATCTAGTCAAATCTCAGTCACATTAGATTTAAGGATTTTTTTTTACAAGCAT-TAGAATAATGTT
256 ATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCT-GAATCATGTT
21245 TCGATTTAATG
320 TCGATTTAATG
* * * * *
21256 AAAAATTAATTTGAAAACAATAGGAAAAACTATTTTAGAAGCGTGAAAAGCTTTTCAGTTTTTTT
1 AGAAATTAATTTGAAAA-AATAGGAAAAACAATATTAGAAGCGTGAAAAGCTTTTCAATCTTTTT
* * * * * *
21321 GGCATTGAATTATATAATTTTTATGAGTGTTGTGCCCCAAAATAGAGGAAAAATTTTTCGGGTCA
65 GGCGTTGAATTATATATTTTTTATGAGTATTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGTCA
* * *
21386 GTTTTTGCAAAATTTTAGCTGAAATCGCGTACTAACCATCACAAATTTTGGCTAAAACTGCGTTT
130 GTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACCATCACAATTTTTGGCTAAAACTGCGTTC
*
21451 CAGGGCCTCGGCTAAGTTTTGCATGATTTTTGGCACCAAGA-TCCTTGAAATATCTATATTCATC
195 CAGGGCC-CGGCTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTTGAAATATCTATATTCATC
* *
21515 TATTCAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAAATCATGTTTCG
259 TAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTG-AATCATGTTTCG
*
21580 ATTTAATA
323 ATTTAATG
* * * * **
21588 AGAAATTATTTTGGACAACAATAGG--AAACGATATTAGAATCGTGAACATCCTTTT-AAT-TTT
1 AGAAATTAATTT-GA-AAAAATAGGAAAAACAATATTAGAAGCGTGAA-AAGCTTTTCAATCTTT
* * * * ** ** **
21649 TTGGCATTAAATTAAATATTTTTTATTAGTATTGTGGCC-AAAATAAATAAAAAAAATTT-GGGT
63 TTGGCGTTGAATTATATATTTTTTATGAGTATTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGT
* * *
21712 -ATGTTTTTGCTAAGTTTTAGCTGAAATCATGTACGT-----T-A-AA----T--C----A-TG-
128 CA-GTTTTTGCAAAATTTTAGCTGAAATCGTGTAC-TAACCATCACAATTTTTGGCTAAAACTGC
* * * *
21757 GTTCCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGTACCAAGACTCCTTGAAATATCTATACT
191 GTTCCAGGG-CCCGGCTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTTGAAATATCTATATT
* * * * * * *
21822 CATCTAATCAAGTCTCAACCACATTAGATTTAATGATTTGTTTTTACGAGCATCTAAATCTTGAT
255 CATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTT
21887 TCGATTTAATG
320 TCGATTTAATG
* ** ** *
21898 AGAAATTAATTCAGAAAAAA-AGGAAAAATGATATTAGAAATGTGAAAAGCCTTTCAATCTTTTT
1 AGAAATTAATT-TGAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCTTTTCAATCTTTTT
* *
21962 GGCGTTGAATTAAATATTTTTTATGAGTATTGTGACCAAAAATT-AGGTAAAAATTTTTCGGGTC
65 GGCGTTGAATTATATATTTTTTATGAGTATTGTGGCCAAAAATTGAGG-AAAAATTTTTCGGGTC
* * * * ** *
22026 AGTTTTTGGAAAACTTTAGCTGAAATTGTGAACTAACCATCACGGTTTTTTTTTTTGCTAAAAAC
129 AGTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACCATCAC-----AATTTTTGGCT-AAAAC
* * * * * * *
22091 -GCGTTCCGGGGTCCCGGCTCAGTTTTACTTGATTTTAGGCGCTC-AGA-TAACTTGAGATATCT
188 TGCGTTCCAGGG-CCCGGCTCAGTTTTGCATGATTTTTGGCAC-CAAGACT-CCTTGAAATATCT
* * * *
22153 ATTTTTATC-ATATCAAATCTCAGCAACATTGGATTTAAGGATTT-TTTTTACGAGCATATGAAT
250 ATATTCATCTA-ATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAAT
* * *
22216 CTTGTTTCGAATTAATA
314 CATGTTTCGATTTAATG
** * * * * * *
22233 AGAAATTAATTCAAACAAAAAATAAAGAGAAACGATATTAGAAGCGTGAAAAGGTCTCCAATCTT
1 AGAAATTAATT---TGAAAAAAT-AGGAAAAACAATATTAGAAGCGTGAAAAGCTTTTCAATCTT
* * * * * *
22298 TTTGGTGTTGAATTATAT-TTTTTTATGAGTATTTTGGCAAAAAATTTAGGAAAAATCTTTCAGG
62 TTTGGCGTTGAATTATATATTTTTTATGAGTATTGTGGCCAAAAATTGAGGAAAAATTTTTCGGG
* * * * * * * * *
22362 TTA-ATTTTGCAAAATTTTAGCCGAATTTGTGCACT-ACCATCACAAATTTTGGCTAAAAATACG
127 TCAGTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACCATCACAATTTTTGGCTAAAACTGCG
* * * * * *
22425 TTTCAGGATCCCGGCTCAGTTTTGCATGATTTTTTGCGCCGATACTCCTTGAAATATCTATATTC
192 TTCCAGG-GCCCGGCTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTTGAAATATCTATATTC
* * *
22490 ATCTAATCAAATCTCAGCCTCATTGAATTTAAGGATTTGTTTTTATC-AGCACCTGAATCATGTT
256 ATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTA-CGAGCATCTGAATCATGTT
22554 TCGATTTAATG
320 TCGATTTAATG
* * * *
22565 AGAAATTAATTTTGAAAACAATAGGAAAAAACGATTTTAGAAGCGTGAAAAGCCCTTT-AATTTT
1 AGAAATTAA-TTTGAAAA-AATAGG-AAAAACAATATTAGAAGCGTGAAAAG-CTTTTCAATCTT
* * * *
22629 TTTGGCGTTCAATTATATATTATTTATGAGTATTGTGGCAAAAAATTGAGTAAAAATTTTTCGGG
62 TTTGGCGTTGAATTATATATTTTTTATGAGTATTGTGGCCAAAAATTGAGGAAAAATTTTTCGGG
* ** * * *
22694 TCAAGTTTTTGCAAAAGTTTAGCTGAAATCGTGTACTAACCATCACGGTTTTTGACTAAAACCGT
127 TC-AGTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACCATCACAATTTTTGGCTAAAACTGC
* * * * * *
22759 GTTCCGGGGCACCGACTCAGTTTTACATGATTTTTGACTCCAACACTCCTTGAAATATATAACTA
191 GTTCCAGGGC-CCGGCTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTTG-AA-ATAT--CTA
* * * * *
22824 TATTTATCTAGTCAAATCTAAGCCACATTGGATTTAAGGATTTGTTTTTACAAGAATCTGAATCA
251 TATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCA
22889 TGCTTT-GATTTAAAT-
316 TG-TTTCGATTT-AATG
* * * * * *
22904 AGAAATTGAATTGGAGAACAATAGGGAAAACAATATT---AGCGTGGAAA-TTTCTTCAA-ATTT
1 AGAAATT-AATTTGA-AAAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCTT-TTCAATCTTT
* *
22964 TTGGTGTTAAATTATATATTTTTTATGAGTATTGTGGCCAAAAATTGAGGAAAAATTTTT-GGGT
63 TTGGCGTTGAATTATATATTTTTTATGAGTATTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGT
* * * ** **
23028 -ATGTTTTTGC-AAATTTCTAGCCGAAATCATGTATTAACCATCACGGTTTTTGGCTAAAACCAC
128 CA-GTTTTTGCAAAATTT-TAGCTGAAATCGTGTACTAACCATCACAATTTTTGGCTAAAACTGC
* * * *
23091 GTTCCAGGGCCCCGGCTTAGTTTTGCATGATTTTCGGCACCGAGACTCTTTGAAATATCTATATT
191 GTTCCAGGG-CCCGGCTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTTGAAATATCTATATT
* * * * * * *
23156 CATCTAAT-AAATTCTCATCCACATTGGATGTAAGGATTTGTTATTATGAGCATCTAAAT-TTGA
255 CATCTAATCAAA-TCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGT
23219 TTCGATTTAATG
319 TTCGATTTAATG
* * *
23231 AGAAATTAATTCGGAAAAAA-AGG-AAAACAATATTAGAAACGTGAAAAACTTTTCAATCTTTTT
1 AGAAATTAATT-TGAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCTTTTCAATCTTTTT
* * *
23294 GGTGTTGAATTATATATTTTCTATGAGTATTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGTAA
65 GGCGTTGAATTATATATTTTTTATGAGTATTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGTCA
* * * * *** * *
23359 GTTCTTGGAAAATTTTAGCTGAAATCATGTATTAACCATCATTTTTTTTGGCAAAAAAC-GCGCT
130 GTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACCATCACAATTTTTGGC-TAAAACTGCGTT
* * * * * * * * * *
23423 CCAGGGTCCCGGCTCATTTTTACATGATTTTAGGCGCCCAGAATACATGAGATATCTATATTTAT
194 CCAGGG-CCCGGCTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTTGAAATATCTATATTCAT
* * * * * *
23488 CTAATTAAATCTCAGCAACATTGGTTTTAAGGATTTGTTTTTACGAGTATCTGAATCTTCTTTCG
258 CTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCG
* *
23553 ATTTGATT
323 ATTTAATG
* * * * *
23561 AGAAATTGATTCAGAAAAAATAAGATAAACAATATTAGAAGCGTGAAAAGCCTTTT-GATCTTTT
1 AGAAATTAATT-TGAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAG-CTTTTCAATCTTTT
* * * * * * *
23625 GGGTGTTGAATTATATAGTTTTAATTAGTATTGTGGCCAAAAACTGAAGAAAAATTTTTCGGGTC
64 TGGCGTTGAATTATATATTTTTTATGAGTATTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGTC
*
23690 AATTTTTGCAAAATTTTAGCTGAAATC
129 AGTTTTTGCAAAATTTTAGCTGAAATC
23717 AAGTACTCCC
Statistics
Matches: 2019, Mismatches: 339, Indels: 206
0.79 0.13 0.08
Matches are distributed among these distances:
308 3 0.00
309 9 0.00
310 87 0.04
311 110 0.05
312 15 0.01
313 29 0.01
314 1 0.00
316 1 0.00
317 1 0.00
318 2 0.00
322 2 0.00
323 1 0.00
324 12 0.01
325 3 0.00
326 13 0.01
327 34 0.02
328 148 0.07
329 158 0.08
330 101 0.05
331 271 0.13
332 468 0.23
333 23 0.01
334 89 0.04
335 116 0.06
336 91 0.05
337 38 0.02
338 49 0.02
339 134 0.07
340 10 0.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (330 bp):
AGAAATTAATTTGAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCTTTTCAATCTTTTTG
GCGTTGAATTATATATTTTTTATGAGTATTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGTCAG
TTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACCATCACAATTTTTGGCTAAAACTGCGTTCC
AGGGCCCGGCTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTTGAAATATCTATATTCATCTA
ATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATT
TAATG
Found at i:22987 original size:667 final size:656
Alignment explanation
Indices: 21001--23717 Score: 2222
Period size: 667 Copynumber: 4.1 Consensus size: 656
20991 CGTTGAATTC
* * ** * **
21001 TATATTTTTTATTAGTATTGTGGCCAAAAGCTGAAGAAAAATTTTTTGAGTCA-AATTTTGCAAA
1 TATATTTTTTATGAGTATTGTGGCAAAAAATTGAGGAAAAATTTTCAG-GT-ATAATTTTGC-AA
* ** * * * * ** *** * * * *
21065 AGTT-TAGATGAAATCGTGTAATAACCATTACAGTTTTTGGCTAAAAATGTGTTCCGGGGCCTCA
63 ATTTCTAGCCGAAATCATGCACTAACCATCACAAATTTTGGCTAAAAACACGTTCCAGGACCCCG
* * * * * *
21129 GCTCAATTTTGTATGATTTATT-GTACCAAGACTCCTTGAGATATCTATATTCATCTAGTCAAAT
128 GCTCAGTTTTGCATGATTT-TTGGCACCGAGACTCCTTGAAATATCTATATTCATCTAATCAAAT
** * ** *
21193 CTCAGTCACATT-AGATTTAAGGATTTTTTTTTA-CAAGCAT-TAGAATAATGTTTCGATTTAAT
192 CTCAACCACATTGA-ATTTAAGGATTTGTTTTTATC-AGCATCTA-AATCTTGATTCGATTTAAT
* * * * * * * *
21255 GAAAAATTAATT-TGAAAACAATAGGAAAAACTATTTTAGAAGCGTGAAAAGCTTTTCAGTTTTT
254 GAGAAATTAATTCAGAAAA-AA-AGGAAAAACGATATTAGAAACGTGAAAAGCCTTTCAATCTTT
* * * * * *
21319 TTGGCATTGAATTATATAATTTTTATGAGTGTTGTGCCCCAAAATAGAGGAAAAATTTTTCGGGT
317 TTGGCGTTGAATTATAT-ATTTTTATGAGTATTGTGGCCAAAAATTGAGTAAAAATTTTTCGGGT
* * * ** *
21384 C-AGTTTTTGCAAAATTTTAGCTGAAATCGCGTACTAACCATCACAAATTTTGGCT-AAAACTGC
381 CAAGTTTTTGGAAAACTTTAGCTGAAATCGTGTACTAACCATCAC-GGTTTTTGCTAAAAAC-GC
* * * * * * * * *
21447 GTTTCAGGGCCTCGGCTAAGTTTTGCATGATTTTTGGCACCAAGATCCTTGAAATATCTATATTC
444 GTTCCGGGGCC-CGGCTCAGTTTTACATGATTTTAGGCGCC-AGATACTTGAGATATCTATATTT
* * *
21512 ATCTATTCAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAAATCATG-T
507 ATCTA-TCAAATCTCAGCAACATTGGATTTAAGGATTTGTTTTTACGAGAATCTG-AATC-TGCT
* *** * * * *
21576 TTCGATTTAATAAGAAATT-ATTTTGGAC-AACAAT--AG-GAAACGATATTAGAATCGTGAACA
569 TTCGATTTAAT-AGAAATTGAATTCAAACAAAAAATAAAGAGAAACAATATT--AAGCGTGAAAA
** **
21636 --TCCTTTTAAT-TTTTTGGCATTAAAT
631 GGT-C-TCCAATATTTTTGGTGTTAAAT
* * * * * **
21661 TAAATATTTTTTATTAGTATTGTGGCCAAAATAAAT-A-AAAAAAATTT-GGGTATGTTTTTGCT
1 T--ATATTTTTTATGAGTATTGTGG-CAAAA-AATTGAGGAAAAATTTTCAGGTATAATTTTGC-
* * * * ** * *
21723 AAGTTT-TAGCTGAAATCATG---T-A-CGT--TAAA---T--C-----A-TGGTTCCGGGGCCC
61 AAATTTCTAGCCGAAATCATGCACTAACCATCACAAATTTTGGCTAAAAACACGTTCCAGGACCC
* * * * *
21769 CGACTCAGTTTTGCATGATTTTTGGTACCAAGACTCCTTGAAATATCTATACTCATCTAATCAAG
126 CGGCTCAGTTTTGCATGATTTTTGGCACCGAGACTCCTTGAAATATCTATATTCATCTAATCAAA
*
21834 TCTCAACCACATT-AGATTTAATGATTTGTTTTTA-CGAGCATCTAAATCTTGATTCGATTTAAT
191 TCTCAACCACATTGA-ATTTAAGGATTTGTTTTTATC-AGCATCTAAATCTTGATTCGATTTAAT
* *
21897 GAGAAATTAATTCAGAAAAAAAGGAAAAATGATATTAGAAATGTGAAAAGCCTTTCAATCTTTTT
254 GAGAAATTAATTCAGAAAAAAAGGAAAAACGATATTAGAAACGTGAAAAGCCTTTCAATCTTTTT
* *
21962 GGCGTTGAATTAAATATTTTTTATGAGTATTGTGACCAAAAATT-AGGTAAAAATTTTTCGGGTC
319 GGCGTTGAATTATATA-TTTTTATGAGTATTGTGGCCAAAAATTGA-GTAAAAATTTTTCGGGTC
* *
22026 -AGTTTTTGGAAAACTTTAGCTGAAATTGTGAACTAACCATCACGGTTTTTTTTTTTGCTAAAAA
382 AAGTTTTTGGAAAACTTTAGCTGAAATCGTGTACTAACCATCACGG------TTTTTGCTAAAAA
*
22090 CGCGTTCCGGGGTCCCGGCTCAGTTTTACTTGATTTTAGGCGCTCAGATAACTTGAGATATCTAT
441 CGCGTTCCGGGG-CCCGGCTCAGTTTTACATGATTTTAGGCGC-CAGAT-ACTTGAGATATCTAT
* * *
22155 TTTTATCATATCAAATCTCAGCAACATTGGATTTAAGGATTT-TTTTTACGAGCATATGAATCTT
503 ATTTATC-TATCAAATCTCAGCAACATTGGATTTAAGGATTTGTTTTTACGAGAATCTGAATC-T
* *
22219 G-TTTCGAATTAATAAGAAATT-AATTCAAACAAAAAATAAAGAGAAACGATATTAGAAGCGTGA
566 GCTTTCGATTTAAT-AGAAATTGAATTCAAACAAAAAATAAAGAGAAACAATATT--AAGCGTGA
* *
22282 AAAGGTCTCCAATCTTTTTGGTGTTGAAT
628 AAAGGTCTCCAATATTTTTGGTGTTAAAT
* *
22311 TATATTTTTTTATGAGTATTTTGGCAAAAAATTTAGGAAAAATCTTTCAGGT-TAATTTTGCAAA
1 TATA-TTTTTTATGAGTATTGTGGCAAAAAATTGAGGAAAAAT-TTTCAGGTATAATTTTGC-AA
* ** * * *
22375 ATTT-TAGCCGAATTTGTGCACT-ACCATCACAAATTTTGGCTAAAAATACGTTTCAGGATCCCG
63 ATTTCTAGCCGAAATCATGCACTAACCATCACAAATTTTGGCTAAAAACACGTTCCAGGACCCCG
* * *
22438 GCTCAGTTTTGCATGATTTTTTGCGCCGATACTCCTTGAAATATCTATATTCATCTAATCAAATC
128 GCTCAGTTTTGCATGATTTTTGGCACCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATC
* * * * * *
22503 TCAGCCTCATTGAATTTAAGGATTTGTTTTTATCAGCACCTGAATCATGTTTCGATTTAATGAGA
193 TCAACCACATTGAATTTAAGGATTTGTTTTTATCAGCATCTAAATCTTGATTCGATTTAATGAGA
** * * *
22568 AATTAATTTTGAAAACAATAGGAAAAAACGATTTTAGAAGCGTGAAAAGCCCTTT-AATTTTTTT
258 AATTAATTCAGAAAA-AA-AGG-AAAAACGATATTAGAAACGTGAAAAG-CCTTTCAATCTTTTT
* *
22632 GGCGTTCAATTATATATTATTTATGAGTATTGTGGCAAAAAATTGAGTAAAAATTTTTCGGGTCA
319 GGCGTTGAATTATATATT-TTTATGAGTATTGTGGCCAAAAATTGAGTAAAAATTTTTCGGGTCA
* * * *
22697 AGTTTTTGCAAAAGTTTAGCTGAAATCGTGTACTAACCATCACGGTTTTTGACTAAAACCGTGTT
383 AGTTTTTGGAAAACTTTAGCTGAAATCGTGTACTAACCATCACGGTTTTTG-CTAAAAACGCGTT
* * * * * * *
22762 CCGGGGCACCGACTCAGTTTTACATGATTTTTGACTCCAACACTCCTTGAAATATATAACTATAT
447 CCGGGGC-CCGGCTCAGTTTTACATGATTTTAGGCGCC-AGA-TACTTG--AGATAT--CTATAT
* * *
22827 TTATCTAGTCAAATCTAAGCCACATTGGATTTAAGGATTTGTTTTTACAAGAATCTGAATCATGC
505 TTATCTA-TCAAATCTCAGCAACATTGGATTTAAGGATTTGTTTTTACGAGAATCTGAATC-TGC
** * * ** * *
22892 TTT-GATTTAAATAGAAATTGAATT-GGA-GAACAATAGGGA-AAACAATATT-AGCGTGGAAAT
568 TTTCGATTT-AATAGAAATTGAATTCAAACAAAAAATAAAGAGAAACAATATTAAGCGTGAAAAG
* *
22952 TTCTTCAA-ATTTTTGGTGTTAAATT
632 GTCTCCAATATTTTTGGTGTTAAA-T
* ** **
22977 ATATATTTTTTATGAGTATTGTGGCCAAAAATTGAGGAAAAATTTTTGGGTATGTTTTTGCAAAT
1 -TATATTTTTTATGAGTATTGTGGCAAAAAATTGAGGAAAAATTTTCAGGTATAATTTTGCAAAT
* * *** * *
23042 TTCTAGCCGAAATCATGTATTAACCATCACGGTTTTTGGCTAAAACCACGTTCCAGGGCCCCGGC
65 TTCTAGCCGAAATCATGCACTAACCATCACAAATTTTGGCTAAAAACACGTTCCAGGACCCCGGC
* * *
23107 TTAGTTTTGCATGATTTTCGGCACCGAGACTCTTTGAAATATCTATATTCATCTAAT-AAATTCT
130 TCAGTTTTGCATGATTTTTGGCACCGAGACTCCTTGAAATATCTATATTCATCTAATCAAA-TCT
* * * * *
23171 CATCCACATTGGATGTAAGGATTTGTTATTATGAGCATCTAAAT-TTGATTCGATTTAATGAGAA
194 CAACCACATTGAATTTAAGGATTTGTTTTTATCAGCATCTAAATCTTGATTCGATTTAATGAGAA
* * * * *
23235 ATTAATTCGGAAAAAAAGG-AAAACAATATTAGAAACGTGAAAAACTTTTCAATCTTTTTGGTGT
259 ATTAATTCAGAAAAAAAGGAAAAACGATATTAGAAACGTGAAAAGCCTTTCAATCTTTTTGGCGT
* *
23299 TGAATTATATATTTTCTATGAGTATTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGT-AAGTTC
324 TGAATTATATATTTT-TATGAGTATTGTGGCCAAAAATTGAGTAAAAATTTTTCGGGTCAAGTTT
* * * *** * *
23363 TTGGAAAATTTTAGCTGAAATCATGTATTAACCATCATTTTTTTTGGCAAAAAACGCGCTCCAGG
388 TTGGAAAACTTTAGCTGAAATCGTGTACTAACCATCACGGTTTTT-GCTAAAAACGCGTTCC-GG
* * *
23428 GTCCCGGCTCATTTTTACATGATTTTAGGCGCCCAGAATACATGAGATATCTATATTTATCTAAT
451 GGCCCGGCTCAGTTTTACATGATTTTAGGCG-CCAG-ATACTTGAGATATCTATATTTATCT-AT
* * * *
23493 TAAATCTCAGCAACATTGGTTTTAAGGATTTGTTTTTACGAGTATCTGAATCTTCTTTCGATTTG
513 CAAATCTCAGCAACATTGGATTTAAGGATTTGTTTTTACGAGAATCTGAATCTGCTTTCGATTT-
* * * * ***
23558 ATTAGAAATTG-ATTC--AGAAAAAAT-AAGATAAACAATATTAGAAGCGTGAAAA-GCCTTTTG
577 AATAGAAATTGAATTCAAACAAAAAATAAAGAGAAACAATATT--AAGCGTGAAAAGGTC-TCCA
* * *
23618 ATCTTTTGGGTGTTGAAT
639 ATATTTTTGGTGTTAAAT
* * * * * * *
23636 TATATAGTTTTAATTAGTATTGTGGCCAAAAACTGAAGAAAAATTTTTCGGGTCA-ATTTTTGCA
1 TATAT--TTTTTATGAGTATTGTGGCAAAAAATTGAGGAAAAA-TTTTCAGGT-ATAATTTTGC-
*
23700 AAATTT-TAGCTGAAATCA
61 AAATTTCTAGCCGAAATCA
23718 AGTACTCCCT
Statistics
Matches: 1688, Mismatches: 270, Indels: 197
0.78 0.13 0.09
Matches are distributed among these distances:
640 2 0.00
641 129 0.08
642 130 0.08
643 8 0.00
645 30 0.02
646 63 0.04
647 59 0.03
648 14 0.01
649 48 0.03
650 40 0.02
651 4 0.00
653 3 0.00
654 2 0.00
655 5 0.00
656 27 0.02
657 75 0.04
658 7 0.00
659 20 0.01
660 69 0.04
661 116 0.07
662 130 0.08
663 5 0.00
664 5 0.00
665 35 0.02
666 152 0.09
667 264 0.16
668 9 0.01
669 16 0.01
670 133 0.08
671 78 0.05
672 10 0.01
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.37
Consensus pattern (656 bp):
TATATTTTTTATGAGTATTGTGGCAAAAAATTGAGGAAAAATTTTCAGGTATAATTTTGCAAATT
TCTAGCCGAAATCATGCACTAACCATCACAAATTTTGGCTAAAAACACGTTCCAGGACCCCGGCT
CAGTTTTGCATGATTTTTGGCACCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCA
ACCACATTGAATTTAAGGATTTGTTTTTATCAGCATCTAAATCTTGATTCGATTTAATGAGAAAT
TAATTCAGAAAAAAAGGAAAAACGATATTAGAAACGTGAAAAGCCTTTCAATCTTTTTGGCGTTG
AATTATATATTTTTATGAGTATTGTGGCCAAAAATTGAGTAAAAATTTTTCGGGTCAAGTTTTTG
GAAAACTTTAGCTGAAATCGTGTACTAACCATCACGGTTTTTGCTAAAAACGCGTTCCGGGGCCC
GGCTCAGTTTTACATGATTTTAGGCGCCAGATACTTGAGATATCTATATTTATCTATCAAATCTC
AGCAACATTGGATTTAAGGATTTGTTTTTACGAGAATCTGAATCTGCTTTCGATTTAATAGAAAT
TGAATTCAAACAAAAAATAAAGAGAAACAATATTAAGCGTGAAAAGGTCTCCAATATTTTTGGTG
TTAAAT
Done.