Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002816.1 Hibiscus syriacus cultivar Beakdansim tig00005794_pilon, 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: 109438
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2857 original size:28 final size:28
Alignment explanation
Indices: 2815--2868 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
2805 TATAATACGT
2815 GTTAGAATTTATTATCAAAATTTTATGG
1 GTTAGAATTTATTATCAAAATTTTATGG
* *
2843 GTTAGAATTTGTTATCAAATTTTTAT
1 GTTAGAATTTATTATCAAAATTTTAT
2869 ATTAATATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (28 bp):
GTTAGAATTTATTATCAAAATTTTATGG
Found at i:14951 original size:12 final size:13
Alignment explanation
Indices: 14936--14968 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
14926 ATAAAATTTA
14936 AATTATAATT-AT
1 AATTATAATTAAT
14948 AATTATAATTAAAT
1 AATTATAATT-AAT
14962 AATTATA
1 AATTATA
14969 TTGAGGGACG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.53
14 9 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AATTATAATTAAT
Found at i:17718 original size:87 final size:87
Alignment explanation
Indices: 17456--17719 Score: 483
Period size: 87 Copynumber: 3.0 Consensus size: 87
17446 TATCTATTTT
*
17456 ATAATATCAGCATCTGAACTCTTGATTTTATTTAAAGGATATAATAATACATTCTACTAGATCAA
1 ATAATATCAGCATCTGAATTCTTGATTTTATTTAAAGGATATAATAATACATTCTACTAGATCAA
17521 TTAATTATTAATGATCTCGTTC
66 TTAATTATTAATGATCTCGTTC
* * *
17543 ACAATATCAGCATTTGAATTCTTGATTTTATTTAAAGGATATAATAATACATTATACTAGATCAA
1 ATAATATCAGCATCTGAATTCTTGATTTTATTTAAAGGATATAATAATACATTCTACTAGATCAA
17608 TTAATTATTAATGATCTCGTTC
66 TTAATTATTAATGATCTCGTTC
*
17630 ATAATATCAACATCTGAATTCTTGATTTTATTTAAAGGATATAATAATACATTCTACTAGATCAA
1 ATAATATCAGCATCTGAATTCTTGATTTTATTTAAAGGATATAATAATACATTCTACTAGATCAA
17695 TTAATTATTAATGATCTCGTTC
66 TTAATTATTAATGATCTCGTTC
17717 ATA
1 ATA
17720 GATGGATCGA
Statistics
Matches: 169, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 169 1.00
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (87 bp):
ATAATATCAGCATCTGAATTCTTGATTTTATTTAAAGGATATAATAATACATTCTACTAGATCAA
TTAATTATTAATGATCTCGTTC
Found at i:20385 original size:18 final size:20
Alignment explanation
Indices: 20358--20400 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
20348 TTGTATTTGG
*
20358 TATATTAAATAATAT-TATA
1 TATATGAAATAATATATATA
20377 -ATATGAAATAATATATATA
1 TATATGAAATAATATATATA
20396 TATAT
1 TATAT
20401 ATATATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 13 0.62
19 4 0.19
20 4 0.19
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
TATATGAAATAATATATATA
Found at i:21555 original size:27 final size:27
Alignment explanation
Indices: 21510--21577 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
21500 ATCCACCTAA
* * *
21510 CTCCGACCCGACCCGAAAATTATATATC
1 CTCC-ACCCGACTCAAAAAATATATATC
* *
21538 CTCCACCTGACTCAAAAAATATATATT
1 CTCCACCCGACTCAAAAAATATATATC
*
21565 CTTCACCCGACTC
1 CTCCACCCGACTC
21578 GAATTTTTAG
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
27 29 0.88
28 4 0.12
ACGTcount: A:0.32, C:0.35, G:0.07, T:0.25
Consensus pattern (27 bp):
CTCCACCCGACTCAAAAAATATATATC
Found at i:34021 original size:37 final size:37
Alignment explanation
Indices: 33945--34021 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 37
33935 TTTTTATATT
*
33945 TTTAATTTTGTAAAAAAAATTACATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTACATAAATATTATCAA
* * * *
33982 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTACATAAATATTAT-CAA
34019 TTT
1 TTT
34022 GTAATATTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
36 12 0.35
37 22 0.65
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTACATAAATATTATCAA
Found at i:34648 original size:21 final size:21
Alignment explanation
Indices: 34618--34681 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
34608 ATTATGACTA
* *
34618 TCGCAATGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCATAAT
* *
34639 TCGCATTGCGATTTACGT-AT
1 TCGCATTGCGATTTTCATAAT
*
34659 TCGCGTTGCGATTTTCATAAT
1 TCGCATTGCGATTTTCATAAT
34680 TC
1 TC
34682 TCAATGTGAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
20 17 0.47
21 19 0.53
ACGTcount: A:0.20, C:0.22, G:0.17, T:0.41
Consensus pattern (21 bp):
TCGCATTGCGATTTTCATAAT
Found at i:34650 original size:41 final size:41
Alignment explanation
Indices: 34596--34681 Score: 95
Period size: 41 Copynumber: 2.1 Consensus size: 41
34586 CAGTTTCCAG
*
34596 ATTCGCAACGCGATTATGAC-TA-TCGCAATGCGATTTTCCTA
1 ATTCGCAACGCGATT-T-ACGTATTCGCAATGCGATTTTCATA
** **
34637 ATTCGCATTGCGATTTACGTATTCGCGTTGCGATTTTCATA
1 ATTCGCAACGCGATTTACGTATTCGCAATGCGATTTTCATA
34678 ATTC
1 ATTC
34682 TCAATGTGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
39 2 0.05
40 3 0.08
41 33 0.87
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.37
Consensus pattern (41 bp):
ATTCGCAACGCGATTTACGTATTCGCAATGCGATTTTCATA
Found at i:35380 original size:33 final size:33
Alignment explanation
Indices: 35334--35430 Score: 140
Period size: 33 Copynumber: 2.9 Consensus size: 33
35324 CAAAATCGCA
** *
35334 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCAATTCTCTCG
*
35367 TTGCGATAGTCATTTCGCGTTGCAATTCTCTCT
1 TTGCGATAGTCATTTCGCGTTGCAATTCTCTCG
*
35400 TTGCGATAGTCATTTCCGCGTTGCCATTCTC
1 TTGCGATAGTCATTT-CGCGTTGCAATTCTC
35431 ATTATCTCGT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
33 44 0.76
34 14 0.24
ACGTcount: A:0.12, C:0.26, G:0.20, T:0.42
Consensus pattern (33 bp):
TTGCGATAGTCATTTCGCGTTGCAATTCTCTCG
Found at i:35432 original size:20 final size:20
Alignment explanation
Indices: 35409--35455 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
35399 TTTGCGATAG
35409 TCATTTCCGCGTTGCCATTC
1 TCATTTCCGCGTTGCCATTC
* * *
35429 TCATTAT-CTCGTTGCGATTT
1 TCATT-TCCGCGTTGCCATTC
35449 TCATTTC
1 TCATTTC
35456 AACCAAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
19 1 0.05
20 20 0.91
21 1 0.05
ACGTcount: A:0.13, C:0.28, G:0.13, T:0.47
Consensus pattern (20 bp):
TCATTTCCGCGTTGCCATTC
Found at i:39042 original size:14 final size:14
Alignment explanation
Indices: 39023--39058 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
39013 ATTGTTTAAT
39023 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
39037 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
39051 TGATTTGT
1 TGATTTGT
39059 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:39210 original size:33 final size:33
Alignment explanation
Indices: 39165--39245 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
39155 ACAAAGTACT
* *
39165 ATCGCAATGCGAAATGAAAATCGTAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
*
39198 ATCGCAACGCGAAATGAAAATCGCAATGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
39231 ATCGCAACGCGAAAT
1 ATCGCAACGCGAAAT
39246 TAAATTTGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:39221 original size:19 final size:18
Alignment explanation
Indices: 39165--39223 Score: 54
Period size: 19 Copynumber: 3.4 Consensus size: 18
39155 ACAAAGTACT
39165 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
* *
39184 ATCGTAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
39198 ATCGCAACGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
39217 ATCGCAA
1 ATCGCAA
39224 TGAGAGAATC
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
14 9 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 16 0.52
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:39297 original size:33 final size:31
Alignment explanation
Indices: 39253--39413 Score: 223
Period size: 33 Copynumber: 4.9 Consensus size: 31
39243 AATTAAATTT
39253 GCGTTGCGATTTTCATTTCGCATTGCGATTC
1 GCGTTGCGATTTTCATTTCGCATTGCGATTC
*
39284 CCTAGTTGCGATTTTCATTTCGCATTGCGAAATTC
1 GC--GTTGCGATTTTCATTTCGCATTGCG--ATTC
39319 GCGTTGCGATTTTCATTTCGCATTGCGAAATTC
1 GCGTTGCGATTTTCATTTCGCATTGCG--ATTC
39352 GCGTTGCGATTTTCATTTCGCATTGCGATTCTC
1 GCGTTGCGATTTTCATTTCGCATTGCGA-T-TC
* *
39385 TCGTTGCGATTTTCATTTCACATTGCGAT
1 GCGTTGCGATTTTCATTTCGCATTGCGAT
39414 AGTAATTTCC
Statistics
Matches: 120, Mismatches: 4, Indels: 11
0.89 0.03 0.08
Matches are distributed among these distances:
31 2 0.02
32 2 0.02
33 111 0.93
35 5 0.04
ACGTcount: A:0.16, C:0.22, G:0.20, T:0.42
Consensus pattern (31 bp):
GCGTTGCGATTTTCATTTCGCATTGCGATTC
Found at i:41721 original size:12 final size:12
Alignment explanation
Indices: 41704--41740 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
41694 TCTTCGGGGA
41704 CTTTTTCTTCTT
1 CTTTTTCTTCTT
41716 CTTTTTCTTCTT
1 CTTTTTCTTCTT
41728 CTTTTTCTTCTT
1 CTTTTTCTTCTT
41740 C
1 C
41741 AGGATTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:41949 original size:24 final size:24
Alignment explanation
Indices: 41915--41968 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
41905 CTGAAACATC
*
41915 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
41939 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
41963 ATCAAA
1 ATCAAA
41969 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:42781 original size:20 final size:21
Alignment explanation
Indices: 42756--42804 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
42746 TCCAAATTCA
*
42756 CAATGCGAA-TAAGTAAATCG
1 CAATGCGAATTAAGAAAATCG
**
42776 CAATGCGAATTTGGAAAATCG
1 CAATGCGAATTAAGAAAATCG
42797 CAATGCGA
1 CAATGCGA
42805 TACTGACTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.20
Consensus pattern (21 bp):
CAATGCGAATTAAGAAAATCG
Found at i:42878 original size:20 final size:20
Alignment explanation
Indices: 42789--42880 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
42779 TGCGAATTTG
* *
42789 GAAAATCGCAATGCGATACT
1 GAAAATCGCAACGAGATACT
** *
42809 GACTATCGCAACGAGATAAT
1 GAAAATCGCAACGAGATACT
* *
42829 ACAAAATCGCAACGAGATTCT
1 -GAAAATCGCAACGAGATACT
*** *
42850 GACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGAGATACT
42870 GAAAATCGCAA
1 GAAAATCGCAA
42881 TCATCTTCAA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (20 bp):
GAAAATCGCAACGAGATACT
Found at i:43195 original size:19 final size:19
Alignment explanation
Indices: 43171--43216 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
43161 TTCTCGTTTA
*
43171 CGATTTTCATTTCGCGTTG
1 CGATTTTCATTTCGCATTG
43190 CGATTTTCATTTCGCATTG
1 CGATTTTCATTTCGCATTG
43209 CGATTTTC
1 CGATTTTC
43217 TCGTTGCGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.13, C:0.22, G:0.17, T:0.48
Consensus pattern (19 bp):
CGATTTTCATTTCGCATTG
Found at i:44854 original size:21 final size:20
Alignment explanation
Indices: 44830--44889 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
44820 AACGGTGGGG
44830 GGGGACTCTTGAGGGA-GGATA
1 GGGGACTCTTGAGGGATGG--A
* **
44851 GGGGCCTCTTGAACGATTGGA
1 GGGGACTCTTGAGGGA-TGGA
44872 GGGGACTCTTGAGGGATG
1 GGGGACTCTTGAGGGATG
44890 ACAGGTGAGT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
23 2 0.06
ACGTcount: A:0.20, C:0.13, G:0.45, T:0.22
Consensus pattern (20 bp):
GGGGACTCTTGAGGGATGGA
Found at i:45298 original size:20 final size:19
Alignment explanation
Indices: 45269--45312 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
45259 CACAATGCGA
45269 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGC-G
* *
45289 AAATGGCTATCGCAATGCG
1 AAATGACTATCGCAACGCG
45308 AAATG
1 AAATG
45313 CAAATCGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.18
Consensus pattern (19 bp):
AAATGACTATCGCAACGCG
Found at i:45355 original size:19 final size:20
Alignment explanation
Indices: 45297--45355 Score: 68
Period size: 19 Copynumber: 3.0 Consensus size: 20
45287 GGAAATGGCT
*
45297 ATCGCAATGCGAAAT-GCAA
1 ATCGCAATGCAAAATCGCAA
* *
45316 ATCGCAACGACAAAATTGCAA
1 ATCGCAATG-CAAAATCGCAA
45337 ATCGCAATG-AAAATCGCAA
1 ATCGCAATGCAAAATCGCAA
45356 TGCGAAATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 17 0.50
20 5 0.15
21 12 0.35
ACGTcount: A:0.46, C:0.22, G:0.17, T:0.15
Consensus pattern (20 bp):
ATCGCAATGCAAAATCGCAA
Found at i:45364 original size:19 final size:19
Alignment explanation
Indices: 45254--45373 Score: 65
Period size: 19 Copynumber: 6.5 Consensus size: 19
45244 CACGAAACTT
*
45254 AAAATCACAATGCGAAAATG
1 AAAATCGCAATGCG-AAATG
** *
45274 ACTATCGCAACGCGGAAATG
1 AAAATCGCAATGC-GAAATG
***
45294 GCTATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
* *
45313 CAAATCGCAA--CG--A-C
1 AAAATCGCAATGCGAAATG
* *
45327 AAAATTGCAAAT-CGCAATG
1 AAAATCGC-AATGCGAAATG
45346 AAAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
45365 -AAATCGCAA
1 AAAATCGCAA
45374 CGACAAAATC
Statistics
Matches: 78, Mismatches: 15, Indels: 16
0.72 0.14 0.15
Matches are distributed among these distances:
14 6 0.08
15 3 0.04
16 2 0.03
17 2 0.03
18 13 0.17
19 26 0.33
20 25 0.32
21 1 0.01
ACGTcount: A:0.44, C:0.21, G:0.19, T:0.16
Consensus pattern (19 bp):
AAAATCGCAATGCGAAATG
Found at i:45411 original size:51 final size:52
Alignment explanation
Indices: 45297--45411 Score: 155
Period size: 51 Copynumber: 2.2 Consensus size: 52
45287 GGAAATGGCT
* **
45297 ATCGCAATGCGAAATGCAAATCGCAACGACAAAATTGCAAATCGCAATGAAA
1 ATCGCAATGCGAAATGCAAATCGCAACGACAAAATCGCAAATCGCAAACAAA
45349 ATCGCAATGCGAAATG-AAATCGCAACGACAAAATCGC-AA-CGCGAAACACAA
1 ATCGCAATGCGAAATGCAAATCGCAACGACAAAATCGCAAATCGC-AAACA-AA
*
45400 ATCGCATTGCGA
1 ATCGCAATGCGA
45412 CTTTCATTTC
Statistics
Matches: 57, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
49 3 0.05
50 5 0.09
51 33 0.58
52 16 0.28
ACGTcount: A:0.44, C:0.23, G:0.18, T:0.14
Consensus pattern (52 bp):
ATCGCAATGCGAAATGCAAATCGCAACGACAAAATCGCAAATCGCAAACAAA
Found at i:45423 original size:19 final size:18
Alignment explanation
Indices: 45401--45464 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
45391 GAAACACAAA
45401 TCGCATTGCGACTTTCATT
1 TCGCATTGCGA-TTTCATT
*
45420 TCGCATTGCGATTT--TG
1 TCGCATTGCGATTTCATT
45436 TCG--TTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
45453 TCGCATTGCGAT
1 TCGCATTGCGAT
45465 AGCCATTTCC
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
14 6 0.16
15 3 0.08
16 4 0.11
17 4 0.11
18 4 0.11
19 17 0.45
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:45471 original size:19 final size:20
Alignment explanation
Indices: 45449--45492 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
45439 TTGCGATTTT
45449 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
* *
45468 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCATTGCGATAGC
45488 CATTT
1 CATTT
45493 TCATGTTGCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:45500 original size:20 final size:20
Alignment explanation
Indices: 45458--45503 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
45448 TCATTTCGCA
*
45458 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCACG
* * *
45478 TTGCGATAGTCATTTTCATG
1 TTGCGATAGCCATTTCCACG
45498 TTGCGA
1 TTGCGA
45504 AAGTAAACTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCACG
Found at i:46011 original size:18 final size:18
Alignment explanation
Indices: 45985--46029 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
45975 GTCGATCAGA
*
45985 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
46003 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
46021 TGATGGCTC
1 TGATGGCTC
46030 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:47397 original size:20 final size:20
Alignment explanation
Indices: 47349--47407 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
47339 AATAGTTTCT
** *
47349 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
47369 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
47389 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
47408 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:47929 original size:20 final size:20
Alignment explanation
Indices: 47904--47955 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
47894 ATTATGTATT
47904 ATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGAAAGTCAGA
*
47924 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAGA
*
47944 ATCTCGTTGCGA
1 ATCGCGTTGCGA
47956 TTTTGTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAGA
Found at i:47992 original size:20 final size:20
Alignment explanation
Indices: 47883--48017 Score: 85
Period size: 20 Copynumber: 6.7 Consensus size: 20
47873 CGCTTTGAAA
*
47883 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTAAGT
* * * *
47904 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTAAGT
* * *
47924 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTAAGT
* * * *
47944 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTAAGT
47965 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTAAGT
* *
47985 ATCTCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTAAGT
*
48005 ATCGCATTACGAT
1 ATCGCATTGCGAT
48018 TTTCCCAATT
Statistics
Matches: 93, Mismatches: 17, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
19 5 0.05
20 63 0.68
21 23 0.25
22 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (20 bp):
ATCGCATTGCGATAGTAAGT
Found at i:48018 original size:61 final size:61
Alignment explanation
Indices: 47883--48020 Score: 177
Period size: 61 Copynumber: 2.3 Consensus size: 61
47873 CGCTTTGAAA
* * * *
47883 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * * *
47944 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCTCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
*
48005 ATCGCATTACGATTTT
1 ATCGCATTGCGATTTT
48021 CCCAATTCGC
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
61 64 1.00
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:48128 original size:21 final size:21
Alignment explanation
Indices: 48088--48128 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
48078 ACTGTAGACC
* *
48088 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATATGCAACT
48109 ATCGCAACGCGATATGCAAC
1 ATCGCAACGCGATATGCAAC
48129 GCGAATTTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (21 bp):
ATCGCAACGCGATATGCAACT
Found at i:50094 original size:60 final size:60
Alignment explanation
Indices: 49968--50080 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 60
49958 AACGGTCCCC
*
49968 CGACTATAGGCTGATACTTTATTAAGTCCATCGACTATTAAAAGTTATAAAATAATCCTT
1 CGACTATAGGCTGATACTTTATTAAGTCCATCGACTATTAAAAGTTACAAAATAATCCTT
* * * *
50028 CAACTATAGAG-TGTTACTTTGTTAAGTTCATCGACTATTAAAAGTTACAAAAT
1 CGACTATAG-GCTGATACTTTATTAAGTCCATCGACTATTAAAAGTTACAAAAT
50081 GGTCACTCGA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
60 46 0.98
61 1 0.02
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.35
Consensus pattern (60 bp):
CGACTATAGGCTGATACTTTATTAAGTCCATCGACTATTAAAAGTTACAAAATAATCCTT
Found at i:54802 original size:2 final size:2
Alignment explanation
Indices: 54797--54828 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
54787 CGTTTTTTTG
54797 TA 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
54829 ATGTTTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:55158 original size:20 final size:19
Alignment explanation
Indices: 55111--55207 Score: 70
Period size: 20 Copynumber: 4.9 Consensus size: 19
55101 GCGATTTTCC
*
55111 GACTATCTCAATGCGAATAT
1 GACTATCGCAATGCG-ATAT
*
55131 GTA-AATCGCAATGCGAGTAT
1 G-ACTATCGCAATGCGA-TAT
*** *
55151 GACTATCGCAACAAGATTCT
1 GACTATCGCAATGCGA-TAT
* *
55171 GACTATCGCAACGCGATGCT
1 GACTATCGCAATGCGAT-AT
55191 GACTATCGCAATGCGAT
1 GACTATCGCAATGCGAT
55208 TTTCAAAGCG
Statistics
Matches: 62, Mismatches: 11, Indels: 8
0.77 0.14 0.10
Matches are distributed among these distances:
19 3 0.05
20 58 0.94
21 1 0.02
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.25
Consensus pattern (19 bp):
GACTATCGCAATGCGATAT
Found at i:55858 original size:20 final size:20
Alignment explanation
Indices: 55788--55875 Score: 88
Period size: 20 Copynumber: 4.5 Consensus size: 20
55778 AGAATCGCAA
*
55788 TGCGATTTT-AGTTTCGCGT
1 TGCGATTTTCATTTTCGCGT
** **
55807 TGCGATAGTCAAATTCGCGT
1 TGCGATTTTCATTTTCGCGT
** *
55827 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
*
55847 TGCGATTTTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
55867 TGCGATTTT
1 TGCGATTTT
55876 AAGTTTCAGA
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
19 7 0.12
20 52 0.88
ACGTcount: A:0.15, C:0.16, G:0.24, T:0.45
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGCGT
Found at i:55882 original size:20 final size:20
Alignment explanation
Indices: 55839--55882 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
55829 CGATAGTCAT
* *
55839 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
55859 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
55879 TTTC
1 TTTC
55883 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:61604 original size:19 final size:19
Alignment explanation
Indices: 61580--61627 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
61570 TAGTTTGCAA
61580 TTTTTTGAAATTTTGGCCT
1 TTTTTTGAAATTTTGGCCT
**** *
61599 TTTTTTTTGTTTTTTGCCT
1 TTTTTTGAAATTTTGGCCT
61618 TTTTTTGAAA
1 TTTTTTGAAA
61628 AAAAAATAGC
Statistics
Matches: 20, Mismatches: 9, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.12, C:0.08, G:0.12, T:0.67
Consensus pattern (19 bp):
TTTTTTGAAATTTTGGCCT
Found at i:61968 original size:11 final size:11
Alignment explanation
Indices: 61944--61977 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
61934 TTGGTGCTGG
61944 AAACAAGATAA
1 AAACAAGATAA
* *
61955 AAATAAGATTA
1 AAACAAGATAA
61966 AAACAAGATAA
1 AAACAAGATAA
61977 A
1 A
61978 GAAAATATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.71, C:0.06, G:0.09, T:0.15
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:63281 original size:18 final size:18
Alignment explanation
Indices: 63258--63307 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
63248 TTTACTCGTA
63258 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
63276 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
63294 ATTTCACTTAGATT
1 ATTTCACTTAGATT
63308 GCTTAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:63480 original size:20 final size:20
Alignment explanation
Indices: 63455--63522 Score: 118
Period size: 20 Copynumber: 3.4 Consensus size: 20
63445 TAGTTTACTT
63455 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
63475 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
**
63495 TCGCAACGCGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
63515 TCGCAACG
1 TCGCAACG
63523 AAAGAATCAC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:63598 original size:20 final size:20
Alignment explanation
Indices: 63581--63640 Score: 111
Period size: 20 Copynumber: 3.0 Consensus size: 20
63571 AATGGTCAAA
63581 TTCACGTTGCGATAGTCATT
1 TTCACGTTGCGATAGTCATT
*
63601 TTCGCGTTGCGATAGTCATT
1 TTCACGTTGCGATAGTCATT
63621 TTCACGTTGCGATAGTCATT
1 TTCACGTTGCGATAGTCATT
63641 CGTGTTGCGA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.40
Consensus pattern (20 bp):
TTCACGTTGCGATAGTCATT
Found at i:63609 original size:40 final size:40
Alignment explanation
Indices: 63565--63640 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
63555 ACGATTCTCT
*
63565 CGTTGCAATGGTCAAATTCACGTTGCGATAGTCATTTTCG
1 CGTTGCAATAGTCAAATTCACGTTGCGATAGTCATTTTCG
* **
63605 CGTTGCGATAGTCATTTTCACGTTGCGATAGTCATT
1 CGTTGCAATAGTCAAATTCACGTTGCGATAGTCATT
63641 CGTGTTGCGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (40 bp):
CGTTGCAATAGTCAAATTCACGTTGCGATAGTCATTTTCG
Found at i:63662 original size:38 final size:39
Alignment explanation
Indices: 63581--63662 Score: 103
Period size: 38 Copynumber: 2.1 Consensus size: 39
63571 AATGGTCAAA
* *
63581 TTCACGTTGCGATAGTCATTTTCGCGTTGCGATAGTCATT
1 TTCACGTTGCGATAGTCA-TTTCGCGTTGCGATAGTAAGT
* **
63621 TTCACGTTGCGATAGTCA-TTCGTGTTGCGATTTTAAGT
1 TTCACGTTGCGATAGTCATTTCGCGTTGCGATAGTAAGT
63659 TTCA
1 TTCA
63663 GATTCTATTC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 19 0.51
40 18 0.49
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.41
Consensus pattern (39 bp):
TTCACGTTGCGATAGTCATTTCGCGTTGCGATAGTAAGT
Found at i:64233 original size:21 final size:20
Alignment explanation
Indices: 64142--64245 Score: 66
Period size: 21 Copynumber: 5.0 Consensus size: 20
64132 GACTCACCTG
*
64142 TCATCGTTCAAGAGG-CCTCC
1 TCATCGTTCAAGAGGCCCT-T
* *
64162 CCTATCGTTCAAGAGGCCCCTA
1 TC-ATCGTTCAAGAGG-CCCTT
** *
64184 TCATCCCTCAAGAGTCCCTT
1 TCATCGTTCAAGAGGCCCTT
* *
64204 CCCACCGTTCAAGAGGCCACTT
1 -TCATCGTTCAAGAGGCC-CTT
*
64226 TCATCGTTGAAGAGGTCCCT
1 TCATCGTTCAAGAGG-CCCT
64246 CCCAACATTC
Statistics
Matches: 63, Mismatches: 15, Indels: 11
0.71 0.17 0.12
Matches are distributed among these distances:
20 5 0.08
21 49 0.78
22 6 0.10
23 3 0.05
ACGTcount: A:0.21, C:0.36, G:0.18, T:0.25
Consensus pattern (20 bp):
TCATCGTTCAAGAGGCCCTT
Found at i:64239 original size:42 final size:42
Alignment explanation
Indices: 64167--64249 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
64157 CCTCCCCTAT
*
64167 CGTTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCTTCCCAC
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCC-TCCCAC
* ** *
64209 CGTTCAAGAGGCCACTTTCATCGTTGAAGAGGTCCCTCCCA
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCA
64250 ACATTCTAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 30 0.86
43 5 0.14
ACGTcount: A:0.22, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCAC
Found at i:65678 original size:14 final size:14
Alignment explanation
Indices: 65641--65702 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
65631 TTGCTTGTTT
*
65641 AATTGATTTATAAA
1 AATTGATTTGTAAA
65655 AATTGATTTGTAAA
1 AATTGATTTGTAAA
* *
65669 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
65684 TATTGATGTGTAAA
1 AATTGATTTGTAAA
65698 TAATT
1 -AATT
65703 CTTATTTGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 13 0.34
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.47
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:65826 original size:20 final size:20
Alignment explanation
Indices: 65817--65854 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
65807 CGCTAAACTC
*
65817 AAAATCGCAATGCGAAAGAT
1 AAAATCGCAACGCGAAAGAT
65837 AAAATCGCAACGCGAAAG
1 AAAATCGCAACGCGAAAG
65855 TCAATTCACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.18, G:0.21, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAGAT
Found at i:65922 original size:20 final size:20
Alignment explanation
Indices: 65897--66141 Score: 246
Period size: 20 Copynumber: 12.8 Consensus size: 20
65887 GCGATTTTCT
* *
65897 CGTTGCGATAGTCAAATACC
1 CGTTGCGATAGTCAAATTCG
*
65917 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
65937 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
65957 CGTTGCGATAGTCAAA-TAG
1 CGTTGCGATAGTCAAATTCG
65976 CCGTTGCGATAGTCAAATTCG
1 -CGTTGCGATAGTCAAATTCG
*
65997 CGTTGCGATAGACAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
66017 CGTTGAGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
*
66031 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
*
66051 TGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
66071 CATTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
* * *
66085 AGTTGCGATAATCAAATTTG
1 CGTTGCGATAGTCAAATTCG
*
66105 CGTTACGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
66125 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
66142 GAATGTGTAA
Statistics
Matches: 186, Mismatches: 25, Indels: 28
0.78 0.10 0.12
Matches are distributed among these distances:
14 21 0.11
16 2 0.01
18 1 0.01
19 2 0.01
20 158 0.85
21 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:66056 original size:54 final size:54
Alignment explanation
Indices: 65917--66133 Score: 272
Period size: 54 Copynumber: 3.9 Consensus size: 54
65907 GTCAAATACC
* *
65917 CGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATAG
1 CGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT--T---TTTG
* * *
65976 CCGTTGCGATAGTCAAATTCGCGTTGCGATAGACAAATTCGCGTTGAGATTTTTG
1 -CGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTG
* * * *
66031 CGTTGCGATAGTCATATTCGTGTTGCGATAGTCAAATTCGCATTGCGATTTTTG
1 CGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTG
* * *
66085 AGTTGCGATAATCAAATTTGCGTTACGATAGTCAAATTCGCGTTGCGAT
1 CGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
66134 ATTCAAATGA
Statistics
Matches: 140, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
54 91 0.65
55 2 0.01
58 1 0.01
60 46 0.33
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (54 bp):
CGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTG
Found at i:66364 original size:140 final size:140
Alignment explanation
Indices: 66112--66381 Score: 506
Period size: 140 Copynumber: 1.9 Consensus size: 140
66102 TTGCGTTACG
66112 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATGTCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATGTCA
* *
66177 TAGCAATGTTCAAACTCAAGTTATTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAACACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66242 AATACACATA
131 AATACACATA
66252 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACA-GATC
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATG-TC
66316 ATAGCAATGTTCAAACTCAAGTTACTAACACATGCCTAACTGAAAATGTTAAAAGTTTACACATA
65 ATAGCAATGTTCAAACTCAAGTTACTAACACATGCCTAACTGAAAATGTTAAAAGTTTACACATA
66381 A
130 A
66382 TACAACGTTT
Statistics
Matches: 127, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
139 1 0.01
140 126 0.99
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATGTCA
TAGCAATGTTCAAACTCAAGTTACTAACACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:66464 original size:18 final size:18
Alignment explanation
Indices: 66441--66475 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
66431 AAGCCGGTTG
*
66441 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
66459 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
66476 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:72414 original size:7 final size:7
Alignment explanation
Indices: 72399--72461 Score: 55
Period size: 7 Copynumber: 9.6 Consensus size: 7
72389 CCCTAAATTG
72399 AAAAA-A
1 AAAAAGA
72405 AAAAAG-
1 AAAAAGA
72411 -AAAAGA
1 AAAAAGA
72417 AAAATA-A
1 AAAA-AGA
*
72424 CAAAAGA
1 AAAAAGA
72431 AAAAAGA
1 AAAAAGA
*
72438 GAAAAGA
1 AAAAAGA
*
72445 GAAAAG-
1 AAAAAGA
72451 AAAAAGA
1 AAAAAGA
72458 AAAA
1 AAAA
72462 TAAGATGGGT
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
5 5 0.11
6 11 0.23
7 30 0.64
8 1 0.02
ACGTcount: A:0.83, C:0.02, G:0.14, T:0.02
Consensus pattern (7 bp):
AAAAAGA
Found at i:72428 original size:14 final size:13
Alignment explanation
Indices: 72398--72466 Score: 70
Period size: 14 Copynumber: 5.2 Consensus size: 13
72388 GCCCTAAATT
72398 GAAAA-AAAAAAA
1 GAAAAGAAAAAAA
72410 GAAAAGAAAAATAA
1 GAAAAGAAAAA-AA
*
72424 CAAAAGAAAAAAGA
1 GAAAAGAAAAAA-A
*
72438 GAAAAG-AGAAAA
1 GAAAAGAAAAAAA
72450 GAAAAAGAAAAATAA
1 G-AAAAGAAAAA-AA
72465 GA
1 GA
72467 TGGGTTCAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
12 7 0.15
13 15 0.32
14 22 0.47
15 3 0.06
ACGTcount: A:0.80, C:0.01, G:0.16, T:0.03
Consensus pattern (13 bp):
GAAAAGAAAAAAA
Found at i:73594 original size:124 final size:123
Alignment explanation
Indices: 73350--73668 Score: 410
Period size: 124 Copynumber: 2.6 Consensus size: 123
73340 CACATGGATT
* * * *
73350 TCAACTTCACGAACGAAGGGGCCATCCACGATTTCAACTTCACAATGAATGATATCATGCCCA-C
1 TCAACTTCACG-ACGAAGGGGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACC
* * *
73414 AACAA-ATTTACTCAAGATTTGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGC
65 AACAACATTCACTCAAGATTGGATTTCAACTTCACGACGAAGGATATACAATTCAAGGC
* * * *
73472 TCAACTTGACGACGAAGGTGTCATCCACGATTTCAACTTCATGACGAAGGATATCGTGCCCACCA
1 TCAACTTCACGACGAAGGGGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACCA
* ** *
73537 TCAACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGGATATATAATTCAAGGC
66 ACAACATTCA-CTCAAGATTGGATTTCAACTTCACGACGAAGGATATACAATTCAAGGC
** * * *
73596 TCAACTTCAAAACGAAGGGGCCATCCATGATTTCAACTTCACGAC-AATGGATATCGTGCTCACA
1 TCAACTTCACGACGAAGGGGCCATCCACGATTTCAACTTCACGACGAA-GGATATCGTGCCCACC
73660 AACAACATT
65 AACAACATT
73669 GGATTTCAAC
Statistics
Matches: 168, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
121 44 0.26
122 15 0.09
123 6 0.04
124 103 0.61
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (123 bp):
TCAACTTCACGACGAAGGGGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACCA
ACAACATTCACTCAAGATTGGATTTCAACTTCACGACGAAGGATATACAATTCAAGGC
Found at i:75735 original size:20 final size:19
Alignment explanation
Indices: 75691--75735 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
75681 ATTTATGTCA
*
75691 TTTTTTTATCTTTTTTTTT
1 TTTTTTTATCTTTTTATTT
*
75710 TATTTTTTATGTTCTTTATTT
1 T-TTTTTTATCTT-TTTATTT
75731 TTTTT
1 TTTTT
75736 AGTTATGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 14 0.64
21 7 0.32
ACGTcount: A:0.09, C:0.04, G:0.02, T:0.84
Consensus pattern (19 bp):
TTTTTTTATCTTTTTATTT
Found at i:80724 original size:81 final size:81
Alignment explanation
Indices: 80599--81157 Score: 751
Period size: 81 Copynumber: 6.9 Consensus size: 81
80589 TTCTAAAATA
80599 AAAGACTAAATGTCTAACTGTGCATTTGGCAGAAATGTGCCAATAATGCAAGTTAGATGAAAGGT
1 AAAGACTAAATGTCTAACTGTGCATTTGGCAGAAATGTGCCAATAATGCAAGTTAGATGAAAGGT
80664 TAAATGCCTTTGGATG
66 TAAATGCCTTTGGATG
* * * * * *
80680 AAAGACTAAATGTCTAATTGTGCATTTGGAAAAAAGGTGTCAATAATTCAAGTTAGATGAAAGGT
1 AAAGACTAAATGTCTAACTGTGCATTTGGCAGAAATGTGCCAATAATGCAAGTTAGATGAAAGGT
* * *
80745 TAAATGTCTTTGAATA
66 TAAATGCCTTTGGATG
** * * *
80761 AAAGACTAAATACCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAATGGG
1 AAAGACTAAATGTCTAACTGTGCATTTGGCAGAAATGTGCCAATAATGCAAGTTAGATGAAAGGT
*
80826 TAAATGCGTTTGGATG
66 TAAATGCCTTTGGATG
* *
80842 AAAGACTAAATGTCTAACTGTGCATTTGGCAGAAATGTGCCAATAATGCAAGATAGATAAAAGGT
1 AAAGACTAAATGTCTAACTGTGCATTTGGCAGAAATGTGCCAATAATGCAAGTTAGATGAAAGGT
* *
80907 TAAATGCCTTTGAATA
66 TAAATGCCTTTGGATG
* * * *
80923 AAAGACTAAATGTCTAACTGTGCATTTAGTAGAAATGTGCCAATAATGCAAGCTAGAAT-AAATG
1 AAAGACTAAATGTCTAACTGTGCATTTGGCAGAAATGTGCCAATAATGCAAGTTAG-ATGAAAGG
80987 TTAAATGCCTTTGGATG
65 TTAAATGCCTTTGGATG
* * * * * * *
81004 AAAGACTAAATGTCTAACTCTGTATTTGGAAAAAATATGTCAATAATGCGAGTTAGATGAAAGGT
1 AAAGACTAAATGTCTAACTGTGCATTTGGCAGAAATGTGCCAATAATGCAAGTTAGATGAAAGGT
*
81069 TAAATGCCTTTGGACG
66 TAAATGCCTTTGGATG
* * * * * *
81085 AAAGACTAAATGTCTAACTATGCTTTTTGGCAGAAAGGTACCATTAATGCAAGTTAGATGAAAAG
1 AAAGACTAAATGTCTAACTGTGC-ATTTGGCAGAAATGTGCCAATAATGCAAGTTAGATGAAAGG
*
81150 TTAGATGC
65 TTAAATGC
81158 ATAACGGTGC
Statistics
Matches: 413, Mismatches: 62, Indels: 5
0.86 0.13 0.01
Matches are distributed among these distances:
80 2 0.00
81 371 0.90
82 40 0.10
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.29
Consensus pattern (81 bp):
AAAGACTAAATGTCTAACTGTGCATTTGGCAGAAATGTGCCAATAATGCAAGTTAGATGAAAGGT
TAAATGCCTTTGGATG
Found at i:81349 original size:46 final size:46
Alignment explanation
Indices: 81209--81342 Score: 207
Period size: 46 Copynumber: 2.9 Consensus size: 46
81199 TTAGATGAAG
81209 AACAGTGCATAATTGGCATGAAAGGATGCCATC-AATGAAAATGTAT
1 AACAGTGCATAATTGGCATGAAAGGATGCCA-CAAATGAAAATGTAT
* * * *
81255 AACAATGCATAATTGGCATGAAATGATGTCATAAATGAAAATGTAT
1 AACAGTGCATAATTGGCATGAAAGGATGCCACAAATGAAAATGTAT
*
81301 AACAGTGCATAATTGACATGAAAGGATGCCACAAATGAAAAT
1 AACAGTGCATAATTGGCATGAAAGGATGCCACAAATGAAAAT
81343 ACATAACGGT
Statistics
Matches: 78, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
46 78 1.00
ACGTcount: A:0.45, C:0.12, G:0.19, T:0.24
Consensus pattern (46 bp):
AACAGTGCATAATTGGCATGAAAGGATGCCACAAATGAAAATGTAT
Found at i:92768 original size:15 final size:15
Alignment explanation
Indices: 92748--92801 Score: 72
Period size: 15 Copynumber: 3.5 Consensus size: 15
92738 GTTTACTTCA
92748 GAATGATTAAGCGCT
1 GAATGATTAAGCGCT
** *
92763 GAATGATTCAAATGTT
1 GAATGATT-AAGCGCT
92779 GAATGATTAAGCGCT
1 GAATGATTAAGCGCT
92794 GAATGATT
1 GAATGATT
92802 CAAATGTTGA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
15 20 0.62
16 12 0.38
ACGTcount: A:0.35, C:0.09, G:0.24, T:0.31
Consensus pattern (15 bp):
GAATGATTAAGCGCT
Found at i:92783 original size:16 final size:16
Alignment explanation
Indices: 92762--92821 Score: 86
Period size: 16 Copynumber: 3.8 Consensus size: 16
92752 GATTAAGCGC
92762 TGAATGATTCAAATGT
1 TGAATGATTCAAATGT
** *
92778 TGAATGATT-AAGCGC
1 TGAATGATTCAAATGT
92793 TGAATGATTCAAATGT
1 TGAATGATTCAAATGT
92809 TGAATGATTCAAA
1 TGAATGATTCAAA
92822 GGCTCTGTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
15 12 0.32
16 25 0.68
ACGTcount: A:0.38, C:0.08, G:0.20, T:0.33
Consensus pattern (16 bp):
TGAATGATTCAAATGT
Found at i:92784 original size:31 final size:31
Alignment explanation
Indices: 92748--92817 Score: 140
Period size: 31 Copynumber: 2.3 Consensus size: 31
92738 GTTTACTTCA
92748 GAATGATTAAGCGCTGAATGATTCAAATGTT
1 GAATGATTAAGCGCTGAATGATTCAAATGTT
92779 GAATGATTAAGCGCTGAATGATTCAAATGTT
1 GAATGATTAAGCGCTGAATGATTCAAATGTT
92810 GAATGATT
1 GAATGATT
92818 CAAAGGCTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.36, C:0.09, G:0.23, T:0.33
Consensus pattern (31 bp):
GAATGATTAAGCGCTGAATGATTCAAATGTT
Found at i:92919 original size:15 final size:15
Alignment explanation
Indices: 92899--92939 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
92889 ACTTCTGTGT
92899 TGAATCATTCAACAC
1 TGAATCATTCAACAC
*
92914 TGAATCATTAAACAC
1 TGAATCATTCAACAC
92929 TGAATCATTCA
1 TGAATCATTCA
92940 GAGGTGCGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.29
Consensus pattern (15 bp):
TGAATCATTCAACAC
Found at i:95485 original size:27 final size:27
Alignment explanation
Indices: 95449--95501 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
95439 TTCATAGCAG
95449 CCACCGTCATTCCCTTACCCGATGCCA
1 CCACCGTCATTCCCTTACCCGATGCCA
*
95476 CCACCGTCATTTCCTTACCCGATGCC
1 CCACCGTCATTCCCTTACCCGATGCC
95502 GCCGCCACCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.17, C:0.47, G:0.11, T:0.25
Consensus pattern (27 bp):
CCACCGTCATTCCCTTACCCGATGCCA
Found at i:95563 original size:33 final size:33
Alignment explanation
Indices: 95500--95563 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 33
95490 TTACCCGATG
* *
95500 CCGCCGCCACCACCATCAGCTGGTTTTATGATC
1 CCGCCGCCACCACCATCAGCAGGTTATATGATC
* *
95533 CCGCCGCCGCCACCGTCA-CAGAGTTATATGA
1 CCGCCGCCACCACCATCAGCAG-GTTATATGA
95564 CCCCTCCTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
32 2 0.08
33 24 0.92
ACGTcount: A:0.20, C:0.39, G:0.20, T:0.20
Consensus pattern (33 bp):
CCGCCGCCACCACCATCAGCAGGTTATATGATC
Found at i:96032 original size:12 final size:13
Alignment explanation
Indices: 95986--96036 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 13
95976 TTTGTATTTA
95986 GTACTTTTTTATT
1 GTACTTTTTTATT
* *
95999 -TAGTTATTTATT
1 GTACTTTTTTATT
*
96011 GGACTTTTTTATT
1 GTACTTTTTTATT
*
96024 GTATTTTTTTATT
1 GTACTTTTTTATT
96037 ATTTATCATT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
12 10 0.33
13 20 0.67
ACGTcount: A:0.18, C:0.04, G:0.10, T:0.69
Consensus pattern (13 bp):
GTACTTTTTTATT
Found at i:96040 original size:11 final size:13
Alignment explanation
Indices: 95962--96036 Score: 57
Period size: 13 Copynumber: 5.8 Consensus size: 13
95952 GCATCGATAG
*
95962 ATTTTTTTATTAT
1 ATTTTTTTATTGT
95975 ATTTGTATTTA--GT
1 ATTT-T-TTTATTGT
*
95988 ACTTTTTTATT-T
1 ATTTTTTTATTGT
* * *
96000 AGTTATTTATTGG
1 ATTTTTTTATTGT
*
96013 ACTTTTTTATTGT
1 ATTTTTTTATTGT
96026 ATTTTTTTATT
1 ATTTTTTTATT
96037 ATTTATCATT
Statistics
Matches: 48, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
11 4 0.08
12 11 0.23
13 28 0.58
14 1 0.02
15 4 0.08
ACGTcount: A:0.20, C:0.03, G:0.08, T:0.69
Consensus pattern (13 bp):
ATTTTTTTATTGT
Found at i:96129 original size:34 final size:34
Alignment explanation
Indices: 96074--96144 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 34
96064 CGTTAATATA
96074 GTTGGATTTATTTTAATTTATTTTG-TTAAATTT
1 GTTGGATTTATTTTAATTTATTTTGCTTAAATTT
*
96107 GTTGGAGTTT-TTGTTAATTTATTTTGCTTAATTTT
1 GTTGGA-TTTATT-TTAATTTATTTTGCTTAAATTT
96142 GTT
1 GTT
96145 TATTACCATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
33 8 0.24
34 16 0.47
35 10 0.29
ACGTcount: A:0.20, C:0.01, G:0.15, T:0.63
Consensus pattern (34 bp):
GTTGGATTTATTTTAATTTATTTTGCTTAAATTT
Done.