Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006884.1 Hibiscus syriacus cultivar Beakdansim tig00017547_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: 87642
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:654 original size:92 final size:93
Alignment explanation
Indices: 458--672 Score: 227
Period size: 92 Copynumber: 2.3 Consensus size: 93
448 CTCAAAGATT
* * *
458 TTTCAAAAGGAACAGACTCAAAGATTTTTCTCAAGAAAAATTGTCTCAAGAGAGACAAAACTTTG
1 TTTCAAAAGAAAC-GACTCAAAGATTTTTCTCAAG-AAAATTGTCTCAAAAGAAACAAAACTTTG
** * * * *
523 TTTCAAAAGATACAAACTCAAAGATTTTTG
64 TTAAAAAAAAAACAAACTCAAAGAATTGTG
* * * * *
553 TTTCAAAAGAAATGACTTAAAGATTTTTTTCACG-AAATTGTCTTAAAAGAAACAAAACTTTGGT
1 TTTCAAAAGAAACGACTCAAAGATTTTTCTCAAGAAAATTGTCTCAAAAGAAACAAAACTTT-GT
* *
617 TAAAAAAAAAACAGACTCAAATAATTGT-
65 TAAAAAAAAAACAAACTCAAAGAATTGTG
* *
645 TTTCCAAAGAAACAACTCAAAGATTTTT
1 TTTCAAAAGAAACGACTCAAAGATTTTT
673 ATTTCAAAAG
Statistics
Matches: 99, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
92 48 0.48
93 22 0.22
94 18 0.18
95 11 0.11
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.30
Consensus pattern (93 bp):
TTTCAAAAGAAACGACTCAAAGATTTTTCTCAAGAAAATTGTCTCAAAAGAAACAAAACTTTGTT
AAAAAAAAAACAAACTCAAAGAATTGTG
Found at i:658 original size:29 final size:29
Alignment explanation
Indices: 620--726 Score: 99
Period size: 29 Copynumber: 3.7 Consensus size: 29
610 CTTTGGTTAA
* *
620 AAAAAAAACAGACTCAAATAATTGT-TTTC
1 AAAAGAAACA-ACTCAAAGAATTGTATTTC
* * *
649 CAAAGAAACAACTCAAAGATTTTTATTTC
1 AAAAGAAACAACTCAAAGAATTGTATTTC
* * * *
678 AAAAGAAACAACTCACAGACTTTTGTTTC
1 AAAAGAAACAACTCAAAGAATTGTATTTC
*
707 AAGAGAAACAAACTCAAAGA
1 AAAAGAAAC-AACTCAAAGA
727 TAGGTTTTGT
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
28 11 0.17
29 45 0.69
30 9 0.14
ACGTcount: A:0.50, C:0.17, G:0.09, T:0.24
Consensus pattern (29 bp):
AAAAGAAACAACTCAAAGAATTGTATTTC
Found at i:738 original size:33 final size:30
Alignment explanation
Indices: 652--777 Score: 141
Period size: 29 Copynumber: 4.2 Consensus size: 30
642 TGTTTTCCAA
* *
652 AGAAACAACTCAAAGAT-TTTTATTTCAAA
1 AGAAACAACTCAAAGATGTTTTGTTTCAAG
* *
681 AGAAACAACTCACAGA-CTTTTGTTTCAAG
1 AGAAACAACTCAAAGATGTTTTGTTTCAAG
710 AGAAACAAACTCAAAGATAGGTTTTGTTTCAAG
1 AGAAAC-AACTCAAAGAT--GTTTTGTTTCAAG
* *
743 GGAAACAATCTCAAAGATG-TTTGTTTTAAG
1 AGAAACAA-CTCAAAGATGTTTTGTTTCAAG
773 AGAAA
1 AGAAA
778 TTGTCTTAAA
Statistics
Matches: 83, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
29 31 0.37
30 23 0.28
31 1 0.01
32 2 0.02
33 26 0.31
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.29
Consensus pattern (30 bp):
AGAAACAACTCAAAGATGTTTTGTTTCAAG
Found at i:942 original size:62 final size:63
Alignment explanation
Indices: 833--961 Score: 201
Period size: 62 Copynumber: 2.1 Consensus size: 63
823 AAGATTTTTC
*
833 TTCAAAAGGAACTGTCTCAAAAGAGGCAAAATTTTGTTTCCAAAGAAACATACTCAAAGATTCT
1 TTCAAAAGAAACTGTCTCAAAAGAGGCAAAATTTTGTTTCCAAAGAAACATACTCAAAGATT-T
*
897 TTCAAAAGAAACTTTCTCAAAAGA-G-AAAATTTTGTTAT-CAAAGAAACATACTCAAAGATTT
1 TTCAAAAGAAACTGTCTCAAAAGAGGCAAAATTTTGTT-TCCAAAGAAACATACTCAAAGATTT
958 TTCA
1 TTCA
962 TTTTGTTTTA
Statistics
Matches: 62, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
61 5 0.08
62 33 0.53
63 2 0.03
64 22 0.35
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.29
Consensus pattern (63 bp):
TTCAAAAGAAACTGTCTCAAAAGAGGCAAAATTTTGTTTCCAAAGAAACATACTCAAAGATTT
Found at i:965 original size:36 final size:36
Alignment explanation
Indices: 925--997 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 36
915 AAAAGAGAAA
*
925 ATTTTGTTATCA-AAGAAACATACTCAAAGATTTTTC
1 ATTTTGTT-TCAGAAGAAACAGACTCAAAGATTTTTC
* **
961 ATTTTGTTTTAGGTGAAACAGACTCAAAGATTTTTC
1 ATTTTGTTTCAGAAGAAACAGACTCAAAGATTTTTC
997 A
1 A
998 ATAAAATCTG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 2 0.06
36 30 0.94
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (36 bp):
ATTTTGTTTCAGAAGAAACAGACTCAAAGATTTTTC
Found at i:1080 original size:30 final size:31
Alignment explanation
Indices: 1026--1084 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
1016 GAGACAGCGT
1026 TTTGTTTCAAAAGAAATAGACTCAAAGATCC
1 TTTGTTTCAAAAGAAATAGACTCAAAGATCC
1057 TTTGTTTCAAAAGAAAT-GACTCAAAGAT
1 TTTGTTTCAAAAGAAATAGACTCAAAGAT
1085 GATGTAGTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 11 0.39
31 17 0.61
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.31
Consensus pattern (31 bp):
TTTGTTTCAAAAGAAATAGACTCAAAGATCC
Found at i:1201 original size:36 final size:35
Alignment explanation
Indices: 1110--1208 Score: 112
Period size: 36 Copynumber: 2.8 Consensus size: 35
1100 TGCAAAAATG
* *
1110 GAAAAATTATC-CAAGTGAGACAACATTTGTTTTTA
1 GAAAAATTATCTCAAGCGAGACAA-AATTGTTTTTA
* * *
1145 GAGAAATTGTCTCAAACGAGACAAAATTGTTTTTGA
1 GAAAAATTATCTCAAGCGAGACAAAATTGTTTTT-A
1181 GAAAAAATTATCTC-AGCGAGACAAAATT
1 G-AAAAATTATCTCAAGCGAGACAAAATT
1209 TTGTTCAAGA
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
35 18 0.34
36 25 0.47
37 10 0.19
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.29
Consensus pattern (35 bp):
GAAAAATTATCTCAAGCGAGACAAAATTGTTTTTA
Found at i:4655 original size:14 final size:15
Alignment explanation
Indices: 4627--4656 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4617 TTAAATGAAT
4627 ATTATGCATAATGCA
1 ATTATGCATAATGCA
4642 ATTATGCA-AATGCA
1 ATTATGCATAATGCA
4656 A
1 A
4657 AAATGTTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (15 bp):
ATTATGCATAATGCA
Found at i:7230 original size:26 final size:28
Alignment explanation
Indices: 7179--7230 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 28
7169 ACAAGTGACT
* *
7179 AAAATGCATAAATCTAAAATACAATATC
1 AAAATGCATAAATATAAAATAAAATATC
7207 AAAAT-CATAAA-ATAAAATAAAATA
1 AAAATGCATAAATATAAAATAAAATA
7231 ATAAAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 11 0.50
27 6 0.27
28 5 0.23
ACGTcount: A:0.65, C:0.10, G:0.02, T:0.23
Consensus pattern (28 bp):
AAAATGCATAAATATAAAATAAAATATC
Found at i:7236 original size:26 final size:27
Alignment explanation
Indices: 7178--7236 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
7168 GACAAGTGAC
* *
7178 TAAAATGCATAAATCTAAAATACAATA
1 TAAAATGCATAAATATAAAATAAAATA
7205 TCAAAAT-CATAAA-ATAAAATAAAATAA
1 T-AAAATGCATAAATATAAAATAAAAT-A
7232 TAAAA
1 TAAAA
7237 AAATCAATCG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
26 14 0.50
27 9 0.32
28 5 0.18
ACGTcount: A:0.66, C:0.08, G:0.02, T:0.24
Consensus pattern (27 bp):
TAAAATGCATAAATATAAAATAAAATA
Found at i:8520 original size:3 final size:3
Alignment explanation
Indices: 8506--8545 Score: 53
Period size: 3 Copynumber: 12.7 Consensus size: 3
8496 TGTGTAACAA
*
8506 AAT AATT AAT AAT AAT AAT AAT AAT AAT ATT AAAT AAT AA
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AA
8546 AAAGAAGACC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 28 0.85
4 5 0.15
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:8691 original size:21 final size:21
Alignment explanation
Indices: 8665--8715 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
8655 CACATGCTCT
8665 TTTGTTTCACCCTCAGAATTA
1 TTTGTTTCACCCTCAGAATTA
8686 TTTGTTTCACCCTCAGAATTA
1 TTTGTTTCACCCTCAGAATTA
8707 TTTGTTTCA
1 TTTGTTTCA
8716 ATTGGACCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.22, C:0.22, G:0.10, T:0.47
Consensus pattern (21 bp):
TTTGTTTCACCCTCAGAATTA
Found at i:13848 original size:2 final size:2
Alignment explanation
Indices: 13841--13882 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
13831 TCCTACACCC
13841 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13883 TCTTGAAAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21393 original size:27 final size:27
Alignment explanation
Indices: 21362--21429 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
21352 TCTATTTACA
21362 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
*
21389 AAATCATATCTCCATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
21416 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
21430 ATTCCTACAC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
25 8 0.21
27 31 0.79
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATGGTAAC
Found at i:25108 original size:27 final size:27
Alignment explanation
Indices: 25077--25144 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
25067 TCTATTTACA
25077 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
25104 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
25131 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
25145 ATTCCTACAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 9 0.22
27 32 0.78
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATGGTAAC
Found at i:37249 original size:16 final size:16
Alignment explanation
Indices: 37225--37258 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
37215 TATCGCCGAC
*
37225 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
37241 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
37257 CG
1 CG
37259 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:44477 original size:20 final size:20
Alignment explanation
Indices: 44452--44544 Score: 87
Period size: 21 Copynumber: 4.5 Consensus size: 20
44442 TTTTCCCAAT
*
44452 TCGCAATGCCAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
44472 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
44493 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
44513 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
44534 TCGCAATGCGA
1 TCGCAATGCGA
44545 TACTTACTAT
Statistics
Matches: 57, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 26 0.46
21 31 0.54
ACGTcount: A:0.40, C:0.19, G:0.24, T:0.17
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:44495 original size:21 final size:21
Alignment explanation
Indices: 44469--44544 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
44459 GCCAATAAGT
44469 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
44490 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
44510 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
*
44531 AAATCGCAATGCGA
1 AAATCGCAACGCGA
44545 TACTTACTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.16
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:44509 original size:41 final size:41
Alignment explanation
Indices: 44452--44544 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
44442 TTTTCCCAAT
*
44452 TCGCAATGCCAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
44493 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
44534 TCGCAATGCGA
1 TCGCAATGCGA
44545 TACTTACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.40, C:0.19, G:0.24, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:44557 original size:41 final size:41
Alignment explanation
Indices: 44471--44605 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
44461 CAATAAGTAA
** *
44471 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
44512 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * ** * *
44553 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
*
44594 TTCGCAACGCGA
1 ATCGCAACGCGA
44606 TACTGACTTT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 5 0.06
41 74 0.91
42 2 0.02
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Found at i:44558 original size:20 final size:20
Alignment explanation
Indices: 44533--44626 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
44523 AATTGGGAAA
*
44533 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * * **
44553 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-TACT
*
44574 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* *
44594 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
*
44614 TTCGCAACGCGAT
1 ATCGCAACGCGAT
44627 TTACATAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:45205 original size:19 final size:19
Alignment explanation
Indices: 45181--45225 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
45171 GCAACGAGAT
* *
45181 AATCGCGACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
45200 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
45219 AATCGCA
1 AATCGCA
45226 TTGCGATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.47, C:0.27, G:0.18, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:45243 original size:19 final size:19
Alignment explanation
Indices: 45221--45404 Score: 156
Period size: 19 Copynumber: 10.1 Consensus size: 19
45211 GAAACCAAAA
*
45221 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
45240 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
45259 TCGCGTTGCGATTTT-TTT
1 TCGCGTTGCGATTTTCATT
45277 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
45297 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
45313 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
45330 TCGCATTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
45344 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
45363 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
45383 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
45403 TC
1 TC
45405 AACCAAAAGA
Statistics
Matches: 134, Mismatches: 17, Indels: 28
0.75 0.09 0.16
Matches are distributed among these distances:
14 19 0.14
15 1 0.01
16 3 0.02
17 3 0.02
18 7 0.05
19 63 0.47
20 37 0.28
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:45329 original size:33 final size:33
Alignment explanation
Indices: 45292--45379 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 33
45282 GTTGCGATTT
* *
45292 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
* *
45325 TCATTTCGCATTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
45358 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
45380 ATTATCTCGT
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 35 0.71
34 14 0.29
ACGTcount: A:0.12, C:0.25, G:0.24, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:45381 original size:20 final size:20
Alignment explanation
Indices: 45347--45404 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
45337 GCGATTCTCT
**
45347 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
45367 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
45387 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
45405 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:47462 original size:42 final size:42
Alignment explanation
Indices: 47402--47524 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
47392 TCCTGACTCG
* * *
47402 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
47444 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
47486 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
47525 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:47482 original size:21 final size:21
Alignment explanation
Indices: 47458--47524 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
47448 TCATTCCTCG
47458 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
47479 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
47500 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
47521 AGAG
1 AGAG
47525 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:48900 original size:14 final size:14
Alignment explanation
Indices: 48881--48916 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
48871 ATTGTTTAAT
48881 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
48895 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
48909 TGATTTGT
1 TGATTTGT
48917 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:49138 original size:19 final size:19
Alignment explanation
Indices: 49116--49207 Score: 78
Period size: 19 Copynumber: 5.4 Consensus size: 19
49106 GATTCCCTCG
49116 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* * *
49135 TTGCGA-----AATTAGCG
1 TTGCGATTTTCATTTCGCA
49149 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
49168 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
49182 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
49201 TTGCGAT
1 TTGCGAT
49208 AGTAATTTCC
Statistics
Matches: 55, Mismatches: 8, Indels: 20
0.66 0.10 0.24
Matches are distributed among these distances:
14 17 0.31
16 7 0.13
17 7 0.13
19 24 0.44
ACGTcount: A:0.16, C:0.21, G:0.20, T:0.43
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:49207 original size:33 final size:33
Alignment explanation
Indices: 49102--49207 Score: 160
Period size: 33 Copynumber: 3.2 Consensus size: 33
49092 TAAATTTGCG
*
49102 TTGCGATTCCCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
* **
49135 TTGCGAAAT-TAGCGTTGCGATTTTCATTTCGCA
1 TTGCG-ATTCTCTCGTTGCGATTTTCATTTCGCA
49168 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
49201 TTGCGAT
1 TTGCGAT
49208 AGTAATTTCC
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
32 2 0.03
33 60 0.94
34 2 0.03
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.42
Consensus pattern (33 bp):
TTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:51733 original size:24 final size:24
Alignment explanation
Indices: 51706--51752 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
51696 CAAAATCCGT
*
51706 GTATTGACCAATATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
51730 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
51753 AATACTGACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:51761 original size:24 final size:24
Alignment explanation
Indices: 51710--51761 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
51700 ATCCGTGTAT
* ** *
51710 TGACCAATATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
51734 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
51758 TGAC
1 TGAC
51762 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:52836 original size:20 final size:20
Alignment explanation
Indices: 52807--52864 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
52797 ATTCATTTGA
*
52807 CTATCACAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
52827 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
52847 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
52865 CGCAATGCGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.40, C:0.22, G:0.21, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:52926 original size:19 final size:19
Alignment explanation
Indices: 52883--53036 Score: 202
Period size: 19 Copynumber: 8.6 Consensus size: 19
52873 GAAATGAAAA
52883 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
52899 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
52916 TTGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
52935 TTGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
52951 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
52968 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
52987 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
53006 TCGCATTGCGATTTCCATT
1 TCGCATTGCGATTTTCATT
*
53025 TCGCGTTGCGAT
1 TCGCATTGCGAT
53037 AGTCTGTTTT
Statistics
Matches: 124, Mismatches: 4, Indels: 17
0.86 0.03 0.12
Matches are distributed among these distances:
14 22 0.18
16 5 0.04
17 5 0.04
19 92 0.74
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:52948 original size:52 final size:52
Alignment explanation
Indices: 52883--53036 Score: 227
Period size: 52 Copynumber: 2.9 Consensus size: 52
52873 GAAATGAAAA
*
52883 TCGCATTGCGATTTTCTCGTTGCGATTTTCATTTTGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
*
52935 TTGCATTGCGATTTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
* *
52987 TCGCATTGCGATTTTCATTTCGCATTGCGATTTCCATTTCGCGTTGCGAT
1 TCGCATTGCGATTTTC---TCG--TTGCGATTTTCATTTCGCATTGCGAT
53037 AGTCTGTTTT
Statistics
Matches: 92, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
52 65 0.71
55 3 0.03
57 24 0.26
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (52 bp):
TCGCATTGCGATTTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
Found at i:55050 original size:19 final size:19
Alignment explanation
Indices: 55026--55091 Score: 89
Period size: 20 Copynumber: 3.5 Consensus size: 19
55016 GAAACTTAAA
55026 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
55045 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCG-AAATGACT
* *
55065 ATCGCAATGCGAAATGA-A
1 ATCGCAACGCGAAATGACT
55083 ATCGCAACG
1 ATCGCAACG
55092 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
18 8 0.20
19 16 0.39
20 17 0.41
ACGTcount: A:0.38, C:0.24, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:55050 original size:39 final size:37
Alignment explanation
Indices: 55007--55142 Score: 112
Period size: 32 Copynumber: 3.9 Consensus size: 37
54997 TAGTTTACTT
*
55007 TCGCAACACGAAACTTAAAATCGCAACGCGAAATGACTA
1 TCGCAACACGAAAC-TAAAATCGCAACGCGAAATGA-AA
* * *** *
55046 TCGCAACGCGAAAATGGCTATCGCAATGCGAAATGAAA
1 TCGCAACACGAAACT-AAAATCGCAACGCGAAATGAAA
55084 TCGC-A-ACG--AC-AAAATCGCAACGCGAAATGAAA
1 TCGCAACACGAAACTAAAATCGCAACGCGAAATGAAA
55116 TCGC-A-ACG--AC-AAAATCGCAACGCGAAA
1 TCGCAACACGAAACTAAAATCGCAACGCGAAA
55143 CACAAATCGC
Statistics
Matches: 83, Mismatches: 13, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
32 45 0.54
34 1 0.01
36 2 0.02
37 1 0.01
38 6 0.07
39 28 0.34
ACGTcount: A:0.43, C:0.25, G:0.19, T:0.12
Consensus pattern (37 bp):
TCGCAACACGAAACTAAAATCGCAACGCGAAATGAAA
Found at i:55098 original size:19 final size:18
Alignment explanation
Indices: 55024--55142 Score: 101
Period size: 14 Copynumber: 6.9 Consensus size: 18
55014 ACGAAACTTA
55024 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
*
55042 ACTATCGCAACGCGAAAATGG
1 A-AATCGCAACGCG-AAAT-G
** *
55063 CTATCGCAATGCGAAATG
1 AAATCGCAACGCGAAATG
*
55081 AAATCGCAA--CGACA--
1 AAATCGCAACGCGAAATG
55095 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
*
55113 AAATCGCAA--CGACA--
1 AAATCGCAACGCGAAATG
55127 AAATCGCAACGCGAAA
1 AAATCGCAACGCGAAA
55143 CACAAATCGC
Statistics
Matches: 83, Mismatches: 9, Indels: 20
0.74 0.08 0.18
Matches are distributed among these distances:
14 18 0.22
16 16 0.19
18 18 0.22
19 15 0.18
20 15 0.18
21 1 0.01
ACGTcount: A:0.44, C:0.24, G:0.20, T:0.12
Consensus pattern (18 bp):
AAATCGCAACGCGAAATG
Found at i:55109 original size:32 final size:32
Alignment explanation
Indices: 55065--55142 Score: 147
Period size: 32 Copynumber: 2.4 Consensus size: 32
55055 GAAAATGGCT
*
55065 ATCGCAATGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
55097 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
55129 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
55143 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATCGCAACGACAAA
Found at i:55171 original size:19 final size:17
Alignment explanation
Indices: 55149--55244 Score: 69
Period size: 19 Copynumber: 5.6 Consensus size: 17
55139 GAAACACAAA
55149 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGA-TTTCATT
*
55168 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
55184 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTTCATT
* *
55200 TTGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
55216 TCG-TTGCGATTTTCATT
1 TCGCTTGCGA-TTTCATT
55233 TCGCATTGCGAT
1 TCGC-TTGCGAT
55245 AGCCATTTCC
Statistics
Matches: 61, Mismatches: 7, Indels: 19
0.70 0.08 0.22
Matches are distributed among these distances:
14 15 0.25
15 3 0.05
16 10 0.16
17 4 0.07
18 13 0.21
19 16 0.26
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (17 bp):
TCGCTTGCGATTTCATT
Found at i:55190 original size:14 final size:14
Alignment explanation
Indices: 55171--55228 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
55161 TTTCATTTCG
55171 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
55185 CGTTGCGATTTCATTTT
1 CGTTGCGA-TT--TTGT
55202 GCGTTGCGATTTTGT
1 -CGTTGCGATTTTGT
55217 CGTTGCGATTTT
1 CGTTGCGATTTT
55229 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 20 0.53
15 5 0.13
17 5 0.13
18 8 0.21
ACGTcount: A:0.09, C:0.16, G:0.26, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:55206 original size:32 final size:33
Alignment explanation
Indices: 55154--55244 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
55144 ACAAATCGCA
55154 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
55187 TTGCGA-TTTCATTTTGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
55219 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
55245 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 31 0.57
33 23 0.43
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:55263 original size:20 final size:19
Alignment explanation
Indices: 55229--55282 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
55219 TTGCGATTTT
*
55229 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
55248 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
55268 CATTTCGTGTTGCGA
1 CATTTCGCGTTGCGA
55283 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:55281 original size:19 final size:19
Alignment explanation
Indices: 55217--55282 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
55207 GCGATTTTGT
**
55217 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
55236 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
55256 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
55275 TGTTGCGA
1 CGTTGCGA
55283 AAGTAAACTA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
19 22 0.56
20 17 0.44
ACGTcount: A:0.15, C:0.23, G:0.24, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:55781 original size:18 final size:18
Alignment explanation
Indices: 55755--55799 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
55745 GTCGATCAGA
* *
55755 TGATGGCTCTGGGTGGGG
1 TGATGGCTCTGGGCGAGG
*
55773 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
55791 TGATGGCTC
1 TGATGGCTC
55800 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.11, C:0.16, G:0.47, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:57142 original size:20 final size:20
Alignment explanation
Indices: 57117--57154 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
57107 AATAGTTTCT
57117 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
57137 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
57155 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:57442 original size:22 final size:22
Alignment explanation
Indices: 57417--57460 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
57407 GATTTAGATA
57417 GACGGATTTCACCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
**
57439 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
57461 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGGATTTCACCGGAGATGGG
Found at i:57719 original size:41 final size:41
Alignment explanation
Indices: 57667--57744 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
57657 CGAAAGTCAG
* * *
57667 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTGTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTGTAT
*
57708 TATCGCATTGCGATAGTAAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
57745 CCCAATTCGC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.38
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTGTAT
Found at i:57741 original size:20 final size:20
Alignment explanation
Indices: 57628--57741 Score: 90
Period size: 20 Copynumber: 5.7 Consensus size: 20
57618 CGCTTTGAAA
57628 ATCGCATTGCGATTATGTAA--
1 ATCGCATTGCGA-TA-GTAAGT
* * *
57648 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTAAGT
* *
57668 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTAAGT
* * * *
57688 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTAAGT
57709 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTAAGT
57729 ATCGCATTGCGAT
1 ATCGCATTGCGAT
57742 TTTCCCAATT
Statistics
Matches: 77, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
18 3 0.04
19 4 0.05
20 56 0.73
21 12 0.16
22 2 0.03
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTAAGT
Found at i:57755 original size:41 final size:41
Alignment explanation
Indices: 57667--57762 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 41
57657 CGAAAGTCAG
* * * * ** *
57667 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTGTAT
1 TATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
57708 TATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAA
1 TATCGCATTGCGATAGTAAGTATCGCATTGCGATTTT-CCAA
57750 T-TCGCATTGCGAT
1 TATCGCATTGCGAT
57763 TTTCCCAATT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 45 0.96
42 2 0.04
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (41 bp):
TATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
Found at i:57756 original size:21 final size:21
Alignment explanation
Indices: 57730--57802 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
57720 ATAGTAAGTA
57730 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
57751 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * * **
57772 TCACGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
57792 TCGCATTGCGA
1 TCGCATTGCGA
57803 ATTGGGAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.19, C:0.26, G:0.16, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:58161 original size:21 final size:20
Alignment explanation
Indices: 58093--58149 Score: 87
Period size: 20 Copynumber: 2.8 Consensus size: 20
58083 TTAAACCTTA
* *
58093 AATTTAAAACCTTAATCTCT
1 AATTTTAAACTTTAATCTCT
58113 AATTTTAAACTTTAATCTCT
1 AATTTTAAACTTTAATCTCT
58133 AATTTTAAACTCTTAAT
1 AATTTTAAACT-TTAAT
58150 TTAAAGTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 29 0.85
21 5 0.15
ACGTcount: A:0.39, C:0.16, G:0.00, T:0.46
Consensus pattern (20 bp):
AATTTTAAACTTTAATCTCT
Found at i:67515 original size:37 final size:38
Alignment explanation
Indices: 67447--67518 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
67437 CCCGAACCTG
67447 ACCCAAATATCACACTTAAAAAACCCCAACCCGACTCT
1 ACCCAAATATCACACTTAAAAAACCCCAACCCGACTCT
*
67485 ACCCGAATATCACACTTAAAAAA-CCCAACCCGAC
1 ACCCAAATATCACACTTAAAAAACCCCAACCCGAC
67519 CCGAACAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
37 11 0.33
38 22 0.67
ACGTcount: A:0.43, C:0.39, G:0.04, T:0.14
Consensus pattern (38 bp):
ACCCAAATATCACACTTAAAAAACCCCAACCCGACTCT
Found at i:75712 original size:60 final size:60
Alignment explanation
Indices: 75626--75807 Score: 199
Period size: 60 Copynumber: 3.1 Consensus size: 60
75616 GCATCATATG
* * * *
75626 TCCCCAAACTAT-AACCTCATTTTAAATTAGTCTTTAAACTTTTGAATATTCCAATTTCA
1 TCCCTAAACTATGACCCTCATTCTAAATTAGTCCTTAAACTTTTGAATATTCCAATTTCA
* * * * * *
75685 T-CATCAAACTATGGCTCTCATTCTAAATTAGCCCTTAAACTTTTGAAAATTCTAATTTCA
1 TCCCT-AAACTATGACCCTCATTCTAAATTAGTCCTTAAACTTTTGAATATTCCAATTTCA
* * ** *
75745 TCCCTAAACTATGACCCTCTTTCTAAATTGGTCCCAAAACTTTTGAATA-TCCAATATCA
1 TCCCTAAACTATGACCCTCATTCTAAATTAGTCCTTAAACTTTTGAATATTCCAATTTCA
75804 TCCC
1 TCCC
75808 CAAATTTATC
Statistics
Matches: 99, Mismatches: 21, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
58 1 0.01
59 20 0.20
60 76 0.77
61 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.37
Consensus pattern (60 bp):
TCCCTAAACTATGACCCTCATTCTAAATTAGTCCTTAAACTTTTGAATATTCCAATTTCA
Found at i:76041 original size:60 final size:60
Alignment explanation
Indices: 75942--76109 Score: 184
Period size: 60 Copynumber: 2.8 Consensus size: 60
75932 TACATTTTTA
* * *
75942 GGATTAAATT-AACATGTTCAAAATGTTTGGGGACTAATTTAGAATAAAGGTCATAGTATGG
1 GGATAAAATTGAACATGTTCAAAA-GTTTGAGGACTAATTTAGAATAAA-GTCATAGTATAG
* * *
76003 GGATGAAATTGAA-ATGTTCAAAAGTTTGAGGACTAATTTAGAATGATAGTCATAGTTTAG
1 GGATAAAATTGAACATGTTCAAAAGTTTGAGGACTAATTTAGAAT-AAAGTCATAGTATAG
* *
76063 GGATAAAATTGGAACAT-TT-AAAAGTTT-AGAGACCAATTTAAAATAAA
1 GGATAAAATT-GAACATGTTCAAAAGTTTGAG-GACTAATTTAGAATAAA
76110 CACCATACTT
Statistics
Matches: 93, Mismatches: 9, Indels: 12
0.82 0.08 0.11
Matches are distributed among these distances:
59 4 0.04
60 59 0.63
61 26 0.28
62 4 0.04
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.32
Consensus pattern (60 bp):
GGATAAAATTGAACATGTTCAAAAGTTTGAGGACTAATTTAGAATAAAGTCATAGTATAG
Found at i:77710 original size:17 final size:17
Alignment explanation
Indices: 77676--77710 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
77666 TTTAAATAGA
*
77676 CTTTTAAACATGTAAGG
1 CTTTTAAACAGGTAAGG
*
77693 CTTTTAAACAGGTCAGG
1 CTTTTAAACAGGTAAGG
77710 C
1 C
77711 CGAACCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31
Consensus pattern (17 bp):
CTTTTAAACAGGTAAGG
Found at i:85676 original size:21 final size:21
Alignment explanation
Indices: 85650--85694 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
85640 TCTCCATCGT
85650 CGTCCGTCGCTTGCCATCCAC
1 CGTCCGTCGCTTGCCATCCAC
* *
85671 CGTCCGTCGCTTGCCGTCCGC
1 CGTCCGTCGCTTGCCATCCAC
85692 CGT
1 CGT
85695 ACTCCGACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.04, C:0.47, G:0.24, T:0.24
Consensus pattern (21 bp):
CGTCCGTCGCTTGCCATCCAC
Done.