Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004642.1 Hibiscus syriacus cultivar Beakdansim tig00010398_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: 142721
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:8035 original size:16 final size:15
Alignment explanation
Indices: 8009--8043 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
7999 GATTAGTTTA
8009 ATTTTTTTATTTATT
1 ATTTTTTTATTTATT
*
8024 ATTTTTTATATTTTTT
1 ATTTTTT-TATTTATT
8040 ATTT
1 ATTT
8044 ATTAGTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (15 bp):
ATTTTTTTATTTATT
Found at i:8763 original size:44 final size:44
Alignment explanation
Indices: 8713--8818 Score: 167
Period size: 44 Copynumber: 2.4 Consensus size: 44
8703 GAAATACAAA
8713 TTAGGAAATAAGTTGGAAAAGCTGGTAATAGCTCCAACATAGTC
1 TTAGGAAATAAGTTGGAAAAGCTGGTAATAGCTCCAACATAGTC
* * * *
8757 TTAGGAAATAAGTTAGAAAGGTTGTTAATAGCTCCAACATAGTC
1 TTAGGAAATAAGTTGGAAAAGCTGGTAATAGCTCCAACATAGTC
*
8801 TTAGGGAATAAGTTGGAA
1 TTAGGAAATAAGTTGGAA
8819 TGTTCTAACA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 56 1.00
ACGTcount: A:0.39, C:0.10, G:0.24, T:0.27
Consensus pattern (44 bp):
TTAGGAAATAAGTTGGAAAAGCTGGTAATAGCTCCAACATAGTC
Found at i:9192 original size:13 final size:11
Alignment explanation
Indices: 9161--9191 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
9151 CCAAAAGAAT
9161 TATATTTTTAA
1 TATATTTTTAA
9172 TATATTTTTAA
1 TATATTTTTAA
9183 TATATTTTT
1 TATATTTTT
9192 TCCTAGGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TATATTTTTAA
Found at i:10902 original size:13 final size:13
Alignment explanation
Indices: 10881--10917 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
10871 GAATCCTTTT
*
10881 TTTCTTTTTTTCC
1 TTTCATTTTTTCC
10894 TTTCATTTTTTCC
1 TTTCATTTTTTCC
*
10907 TTTCGTTTTTT
1 TTTCATTTTTT
10918 ACAAGATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.76
Consensus pattern (13 bp):
TTTCATTTTTTCC
Found at i:23939 original size:5 final size:5
Alignment explanation
Indices: 23929--23974 Score: 92
Period size: 5 Copynumber: 9.2 Consensus size: 5
23919 AGAGAAATAA
23929 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A
23975 TGGAGAATAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:29769 original size:78 final size:78
Alignment explanation
Indices: 29630--29787 Score: 244
Period size: 78 Copynumber: 2.0 Consensus size: 78
29620 TCAGATCTCG
* * * * *
29630 AACCCACAGAGAATGTATCTCACAAAATAGTTGTTGTTGGCAAAAAGATAAGTAATATGTATTTT
1 AACCCACAGAGAATGTATATCACAAAAGAGTTGTTATTGGCAAAAAGAGAAGAAATATGTATTTT
*
29695 AAGAATGTAAGAA
66 AAGAAAGTAAGAA
* *
29708 AACCCACAGAGAGTGTATATCACAAAAGAGTTGTTATTGGCAAAAAGAGAAGAAATGTGTATTTT
1 AACCCACAGAGAATGTATATCACAAAAGAGTTGTTATTGGCAAAAAGAGAAGAAATATGTATTTT
29773 AAGAAAGTAAGAA
66 AAGAAAGTAAGAA
29786 AA
1 AA
29788 ATATAGAAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
78 72 1.00
ACGTcount: A:0.46, C:0.09, G:0.20, T:0.25
Consensus pattern (78 bp):
AACCCACAGAGAATGTATATCACAAAAGAGTTGTTATTGGCAAAAAGAGAAGAAATATGTATTTT
AAGAAAGTAAGAA
Found at i:33296 original size:20 final size:20
Alignment explanation
Indices: 33271--33344 Score: 71
Period size: 20 Copynumber: 3.6 Consensus size: 20
33261 GTAATTAGCG
33271 TTGCGAAATTGAGAACCGCT
1 TTGCGAAATTGAGAACCGCT
* *
33291 TTGCGAATTTGGAGAATCGCT
1 TTGCGAAATT-GAGAACCGCT
* *
33312 TTGCGAATTTG-GAAACTG-T
1 TTGCGAAATTGAG-AACCGCT
33331 GTTGCGAAATTGAG
1 -TTGCGAAATTGAG
33345 TTCGCGTTGC
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
19 2 0.04
20 23 0.51
21 20 0.44
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (20 bp):
TTGCGAAATTGAGAACCGCT
Found at i:33311 original size:21 final size:21
Alignment explanation
Indices: 33271--33324 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
33261 GTAATTAGCG
*
33271 TTGCGAAATT-GAGAACCGCT
1 TTGCGAATTTGGAGAACCGCT
*
33291 TTGCGAATTTGGAGAATCGCT
1 TTGCGAATTTGGAGAACCGCT
33312 TTGCGAATTTGGA
1 TTGCGAATTTGGA
33325 AACTGTGTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 9 0.29
21 22 0.71
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (21 bp):
TTGCGAATTTGGAGAACCGCT
Found at i:33316 original size:99 final size:98
Alignment explanation
Indices: 33109--33338 Score: 300
Period size: 99 Copynumber: 2.3 Consensus size: 98
33099 ATTGGCTATT
*
33109 TCGCGTTGCGAATTTGAAAACTGAGTTGCGAATAGTTGTGTTTACCTATATCGGTAATTAGTGTT
1 TCGCGTTGCGAATTTGAAAACTGAGTTGCGAATAGTTGTGTTTACCTATATCGGTAATTAGCGTT
* *
33174 ACGAATTTGGAGAATCGCGTTACAAATTTGAAA
66 ACGAAATTGGAGAACCGCGTTACAAATTTGAAA
* * * *
33207 ACTGAGTTGCGATTTTGAAAACTGAGTTGTGAATAGTTGTGTTTACCTATATCGGTAATTAGCGT
1 TC-GCGTTGCGAATTTGAAAACTGAGTTGCGAATAGTTGTGTTTACCTATATCGGTAATTAGCGT
* * * *
33272 TGCGAAATT-GAGAACCGCTTTGCGAATTTGGAGAA
65 TACGAAATTGGAGAACCGCGTTACAAATTT-GA-AA
* * *
33307 TCGCTTTGCGAATTTGGAAACTGTGTTGCGAA
1 TCGCGTTGCGAATTTGAAAACTGAGTTGCGAA
33339 ATTGAGTTCG
Statistics
Matches: 111, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
98 17 0.15
99 91 0.82
100 3 0.03
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.34
Consensus pattern (98 bp):
TCGCGTTGCGAATTTGAAAACTGAGTTGCGAATAGTTGTGTTTACCTATATCGGTAATTAGCGTT
ACGAAATTGGAGAACCGCGTTACAAATTTGAAA
Found at i:34117 original size:24 final size:22
Alignment explanation
Indices: 34077--34122 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 22
34067 TTGTTTGAAT
34077 TTAAAATTTTAAAAAAATATTA
1 TTAAAATTTTAAAAAAATATTA
*
34099 TTAAAATTATTTAATAAAATATTA
1 TTAAAA-T-TTTAAAAAAATATTA
34123 GAATAATTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 6 0.29
23 1 0.05
24 14 0.67
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TTAAAATTTTAAAAAAATATTA
Found at i:34130 original size:24 final size:24
Alignment explanation
Indices: 34084--34131 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
34074 AATTTAAAAT
*
34084 TTTAAAAAAATATTATTAAAATTA
1 TTTAAAAAAATATTATGAAAATTA
*
34108 TTTAATAAAATATTA-GAATAATTA
1 TTTAAAAAAATATTATGAA-AATTA
34132 GATATAGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (24 bp):
TTTAAAAAAATATTATGAAAATTA
Found at i:34638 original size:44 final size:44
Alignment explanation
Indices: 34563--34664 Score: 143
Period size: 44 Copynumber: 2.3 Consensus size: 44
34553 ACATGGGCTG
* *
34563 TTGCTTCATCTTCTTCCTTTTACTCAGGTAGTTATCATGAGTTC
1 TTGCTTCATCTTCTTCCTTTTACTCAGGTAGTTACCATCAGTTC
* * *
34607 TTGTTTCATCTTCTTCCTTTTTCT-TGAGTAGTTACCATCAGTTC
1 TTGCTTCATCTTCTTCCTTTTACTCAG-GTAGTTACCATCAGTTC
34651 TTGCTTCATCTTCT
1 TTGCTTCATCTTCT
34665 ACTATTATCC
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
43 1 0.02
44 50 0.98
ACGTcount: A:0.14, C:0.24, G:0.12, T:0.51
Consensus pattern (44 bp):
TTGCTTCATCTTCTTCCTTTTACTCAGGTAGTTACCATCAGTTC
Found at i:35346 original size:2 final size:2
Alignment explanation
Indices: 35339--35369 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
35329 TTTGGAAATG
35339 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35370 TTAAAAGCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35401 original size:51 final size:51
Alignment explanation
Indices: 35299--35403 Score: 126
Period size: 51 Copynumber: 2.1 Consensus size: 51
35289 CATTTTAAAA
* * *
35299 ATATATATAATATATAGTCTTTGAAAACATTTTGGAAATGTATATATATAT
1 ATATATATAATATATAGTATTTGAAAACATTTTGAAAACGTATATATATAT
*
35350 ATATATATATATATATA-TATTT-AAAAGCATTTTTTAAAACGTATATA-ATAT
1 ATATATATA-ATATATAGTATTTGAAAA-CA-TTTTGAAAACGTATATATATAT
35401 ATA
1 ATA
35404 GTTTTGAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
50 4 0.09
51 22 0.47
52 21 0.45
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.44
Consensus pattern (51 bp):
ATATATATAATATATAGTATTTGAAAACATTTTGAAAACGTATATATATAT
Found at i:35421 original size:38 final size:38
Alignment explanation
Indices: 35353--35491 Score: 124
Period size: 38 Copynumber: 3.6 Consensus size: 38
35343 TATATATATA
* * *
35353 TATATATATATATA-TATTT-AAAAGCATTTTTTAAAACG
1 TATATA-ATATATAGT-TTTGAAAAACCTTTTTTAAAACT
*
35391 TATATAATATATAGTTTTGAAAAACCTTTTTTGAAAATT
1 TATATAATATATAGTTTTGAAAAACCTTTTTT-AAAACT
* * *
35430 TATATGATATATAGTTTTG-AAAA-CATTTTGAAAACATT
1 TATATAATATATAGTTTTGAAAAACCTTTTTTAAAAC--T
* *
35468 TATATATTATATAGTTTTTAAAAA
1 TATATAATATATAGTTTTGAAAAA
35492 TGTATATATT
Statistics
Matches: 84, Mismatches: 11, Indels: 11
0.79 0.10 0.10
Matches are distributed among these distances:
36 4 0.05
37 15 0.18
38 39 0.46
39 26 0.31
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.45
Consensus pattern (38 bp):
TATATAATATATAGTTTTGAAAAACCTTTTTTAAAACT
Found at i:35460 original size:11 final size:11
Alignment explanation
Indices: 35444--35468 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
35434 TGATATATAG
35444 TTTTGAAAACA
1 TTTTGAAAACA
35455 TTTTGAAAACA
1 TTTTGAAAACA
35466 TTT
1 TTT
35469 ATATATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:35613 original size:8 final size:7
Alignment explanation
Indices: 35589--35641 Score: 53
Period size: 6 Copynumber: 8.0 Consensus size: 7
35579 TTTTTAAAAA
35589 ATATT-T
1 ATATTAT
35595 ATA-TAT
1 ATATTAT
35601 ATATTAT
1 ATATTAT
35608 ACTATTAT
1 A-TATTAT
35616 ATTATTAT
1 A-TATTAT
35624 -TATTAT
1 ATATTAT
35630 -TATTAT
1 ATATTAT
35636 -TATTAT
1 ATATTAT
35642 TAGTGTAATT
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
5 1 0.02
6 25 0.58
7 4 0.09
8 13 0.30
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (7 bp):
ATATTAT
Found at i:35623 original size:3 final size:3
Alignment explanation
Indices: 35610--35671 Score: 67
Period size: 3 Copynumber: 21.3 Consensus size: 3
35600 TATATTATAC
* * *
35610 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAG TGT AAT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
35656 TAT T-T ATAT TAT TAT T
1 TAT TAT -TAT TAT TAT T
35672 TCTTATTTAA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
2 5 0.10
3 43 0.88
4 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:37014 original size:16 final size:16
Alignment explanation
Indices: 36993--37025 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
36983 CCTAAATTTA
36993 TTTTATTA-TTATTGTT
1 TTTTATTACTT-TTGTT
37009 TTTTATTACTTTTGTT
1 TTTTATTACTTTTGTT
37025 T
1 T
37026 ATTTTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.15, C:0.03, G:0.06, T:0.76
Consensus pattern (16 bp):
TTTTATTACTTTTGTT
Found at i:37153 original size:3 final size:3
Alignment explanation
Indices: 37145--37169 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
37135 TCTAGTTAAT
37145 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
37170 ATTTTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:38902 original size:19 final size:19
Alignment explanation
Indices: 38868--38912 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
38858 ATTTAGACAT
38868 TTTGCA-TTTCTTATTTTC
1 TTTGCATTTTCTTATTTTC
*
38886 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTCTTATTTTC
38905 TTTGCATT
1 TTTGCATT
38913 CATATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.11, C:0.13, G:0.09, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTCTTATTTTC
Found at i:43116 original size:165 final size:165
Alignment explanation
Indices: 42258--43076 Score: 1426
Period size: 165 Copynumber: 5.0 Consensus size: 165
42248 TTAACAAACT
42258 ATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCTAACAAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCTAACAAAAGACCTTTGAGTTCGACTACG
*
42323 CTCAGCTTCGAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAGGGCTATCTGCCAAAGACC
66 CTCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAGGGCTATCTGCCAAAGACC
*
42388 CCCGAGTTCGATCACACTCAGCTTCGAGGGCACATC
130 CCCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
42424 ATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCTAACAAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCTAACAAAAGACCTTTGAGTTCGACTACG
*
42489 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
66 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAGGGCTATCTGCCAAAGACCC
42554 CCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
131 CCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
* * * * * * *
42589 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG-TGACCAAAAGACCTTCGAGTTCGACTAC
1 ATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCT-AACAAAAGACCTTTGAGTTCGACTAC
42653 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAGGGCTATCTGCCAAAGACC
65 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAGGGCTATCTGCCAAAGACC
*
42718 CCCGAGTTCGATCACACTCAGCTTCGAGGGCACATC
130 CCCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
42754 ATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCTAACAAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCTAACAAAAGACCTTTGAGTTCGACTACG
* *
42819 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAGGACCC
66 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAGGGCTATCTGCCAAAGACCC
*
42884 CCAAGTTCGATTACACTCAGCTTCGAGGGCACATC
131 CCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
** *
42919 ATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTG-TCGCCAAAAGACCTTCGAGTTCGACTAC
1 ATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCT-AACAAAAGACCTTTGAGTTCGACTAC
*
42983 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAGGGCTATCTGCCAAGGACC
65 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAGGGCTATCTGCCAAAGACC
*
43048 CCCGAGTTCGATTACACTCAACTTCGAGG
130 CCCGAGTTCGATTACACTCAGCTTCGAGG
43077 TCATATCGTT
Statistics
Matches: 621, Mismatches: 29, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
164 2 0.00
165 547 0.88
166 72 0.12
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (165 bp):
ATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCTAACAAAAGACCTTTGAGTTCGACTACG
CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAGGGCTATCTGCCAAAGACCC
CCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
Found at i:43854 original size:2 final size:2
Alignment explanation
Indices: 43843--43878 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
43833 TTTGGAAATG
43843 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
43879 TTAAAAGCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:43928 original size:36 final size:38
Alignment explanation
Indices: 43864--43958 Score: 101
Period size: 36 Copynumber: 2.6 Consensus size: 38
43854 TATATATATA
* *
43864 TATAT-ATATATA-TATTT-AAAAGCATTTTTTAAAACG
1 TATATGATATATAGT-TTTGAAAAACCTTTTTTAAAACG
* **
43900 TATAT-A-ATATAGTTTTGAAAAACCTTTTTTGAAATT
1 TATATGATATATAGTTTTGAAAAACCTTTTTTAAAACG
43936 TATATGATATATAGTTTTGAAAA
1 TATATGATATATAGTTTTGAAAA
43959 CATTTTGAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
35 8 0.16
36 26 0.52
37 1 0.02
38 15 0.30
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.45
Consensus pattern (38 bp):
TATATGATATATAGTTTTGAAAAACCTTTTTTAAAACG
Found at i:43966 original size:11 final size:11
Alignment explanation
Indices: 43950--43974 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
43940 TGATATATAG
43950 TTTTGAAAACA
1 TTTTGAAAACA
43961 TTTTGAAAACA
1 TTTTGAAAACA
43972 TTT
1 TTT
43975 ATATATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:43975 original size:38 final size:36
Alignment explanation
Indices: 43864--43994 Score: 99
Period size: 36 Copynumber: 3.6 Consensus size: 36
43854 TATATATATA
** **
43864 TATATATATATA-TATTT-AAAAGCATTTTTTAAAACG
1 TATATATATATAGT-TTTGAAAA-CATTTTGAAAAATT
* ***
43900 TATATA-ATATAGTTTTGAAAAACCTTTTTTGAAATT
1 TATATATATATAGTTTTG-AAAACATTTTGAAAAATT
43936 TATATGATATATAGTTTTGAAAACATTTTGAAAACATT
1 TATAT-ATATATAGTTTTGAAAACATTTTGAAAA-ATT
* *
43974 TATATAT-TATATTTTTAAAAA
1 TATATATATATAGTTTTGAAAA
43995 TGTATATATA
Statistics
Matches: 79, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
35 8 0.10
36 34 0.43
37 18 0.23
38 19 0.24
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.46
Consensus pattern (36 bp):
TATATATATATAGTTTTGAAAACATTTTGAAAAATT
Found at i:44033 original size:129 final size:128
Alignment explanation
Indices: 43807--44073 Score: 281
Period size: 133 Copynumber: 2.1 Consensus size: 128
43797 ATTTTAAAAA
* * *
43807 TATATATATATAGTCTTTGAAAACATTTTGGAAATGTATAATATATATATATATATATATATATA
1 TATATATATATAGTCTTTGAAAACATTTTGAAAATGTATAATATATATATAAAAATATATATATA
43872 TATATATTTAAAAGCATTTTTTAAAACGTATATAATATAGTTTTGAAAAACCTTTTTTGAAATT
66 TATATATTTAAAAGCATTTTTTAAAAC-TATATAATATAGTTTTGAAAAACCTTTTTTGAAATT
* * * *
43936 TATATGATATATAGT-TTTGAAAACATTTTGAAAACATTTATATATTATATTTTTAAAAATGTAT
1 TATAT-ATATATAGTCTTTGAAAACATTTTG-AAA-ATGTATA-A-TATATATATAAAAATATAT
* * * * * * ** * *
44000 ATATAT-TTTTTTTTAAAGCATTTTTTTAATA-TATATTATATAATTTAAAAAAAAACATTTTTG
61 ATATATATATATTTAAAAGCA-TTTTTTAAAACTATATAATATAGTTT-TGAAAAACCTTTTTTG
44063 AAA-T
124 AAATT
44067 TATATAT
1 TATATAT
44074 TATGTTTTTT
Statistics
Matches: 114, Mismatches: 17, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
129 20 0.18
130 13 0.11
131 25 0.22
132 27 0.24
133 29 0.25
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (128 bp):
TATATATATATAGTCTTTGAAAACATTTTGAAAATGTATAATATATATATAAAAATATATATATA
TATATATTTAAAAGCATTTTTTAAAACTATATAATATAGTTTTGAAAAACCTTTTTTGAAATT
Found at i:44120 original size:3 final size:3
Alignment explanation
Indices: 44107--44169 Score: 76
Period size: 3 Copynumber: 21.3 Consensus size: 3
44097 ATATATATAC
* * *
44107 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAG TGT AAT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
44153 TATT TAT TAT TAT TAT T
1 TA-T TAT TAT TAT TAT T
44170 TCTTATTTAA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
2 4 0.08
3 44 0.86
4 3 0.06
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:44175 original size:7 final size:7
Alignment explanation
Indices: 44107--44178 Score: 50
Period size: 6 Copynumber: 10.9 Consensus size: 7
44097 ATATATATAC
44107 TATTATAT
1 TATT-TAT
44115 TA-TTAT
1 TATTTAT
44121 TA-TTAT
1 TATTTAT
44127 TA-TTAT
1 TATTTAT
44133 TA-TTAT
1 TATTTAT
*
44139 TAGTGTAAT
1 TA-T-TTAT
44148 TA-TT-T
1 TATTTAT
44153 TATTTAT
1 TATTTAT
44160 TA-TTAT
1 TATTTAT
*
44166 TATTTCT
1 TATTTAT
44173 TATTTA
1 TATTTA
44179 ATCATTTTTG
Statistics
Matches: 54, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
5 3 0.06
6 32 0.59
7 12 0.22
8 2 0.04
9 5 0.09
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (7 bp):
TATTTAT
Found at i:44186 original size:33 final size:33
Alignment explanation
Indices: 44123--44186 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
44113 ATTATTATTA
*
44123 TTATTATTATTATTATTAGTGTAATTATTTTAT
1 TTATTATTATTATTATTAGTGTAATCATTTTAT
* *
44156 TTATTATTATTATTTCTTA-TTTAATCATTTT
1 TTATTATTATTA-TTATTAGTGTAATCATTTT
44187 TGTTTTATGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 22 0.81
34 5 0.19
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (33 bp):
TTATTATTATTATTATTAGTGTAATCATTTTAT
Found at i:45510 original size:16 final size:16
Alignment explanation
Indices: 45489--45521 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
45479 CCTAAATTTA
45489 TTTTATTA-TTATTGTT
1 TTTTATTACTT-TTGTT
45505 TTTTATTACTTTTGTT
1 TTTTATTACTTTTGTT
45521 T
1 T
45522 ATTTTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.15, C:0.03, G:0.06, T:0.76
Consensus pattern (16 bp):
TTTTATTACTTTTGTT
Found at i:45649 original size:3 final size:3
Alignment explanation
Indices: 45641--45672 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
45631 TCTAGTTAAT
45641 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
45673 TTTTTTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:46416 original size:19 final size:19
Alignment explanation
Indices: 46392--46439 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
46382 TGTTAACTAC
46392 TGAAGAAAGAGGAAGATGA
1 TGAAGAAAGAGGAAGATGA
46411 TGAAGAAAGAGGAAGATGA
1 TGAAGAAAGAGGAAGATGA
*
46430 TGAAGCAAGA
1 TGAAGAAAGA
46440 ACCCATAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.52, C:0.02, G:0.35, T:0.10
Consensus pattern (19 bp):
TGAAGAAAGAGGAAGATGA
Found at i:47505 original size:26 final size:26
Alignment explanation
Indices: 47475--47555 Score: 146
Period size: 26 Copynumber: 3.1 Consensus size: 26
47465 AAAATTATTT
47475 TTTATTTTATTATTTTTTCAAATTCA
1 TTTATTTTATTATTTTTTCAAATTCA
47501 TTTATTTTATTATTTTTTCAAATTCA
1 TTTATTTTATTATTTTTTCAAATTCA
47527 TTTATTTT-TTATTTTTTTCAAATTCA
1 TTTATTTTATTA-TTTTTTCAAATTCA
47553 TTT
1 TTT
47556 TTATTACGTG
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
25 3 0.06
26 51 0.94
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (26 bp):
TTTATTTTATTATTTTTTCAAATTCA
Found at i:48244 original size:18 final size:18
Alignment explanation
Indices: 48221--48267 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
48211 GTTTGTGGTC
48221 GAAGCGTGAGATTCGTCT
1 GAAGCGTGAGATTCGTCT
48239 GAAGCGTGAGATTCGTCT
1 GAAGCGTGAGATTCGTCT
48257 GAAGCGTGAGA
1 GAAGCGTGAGA
48268 CTAATAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.26, C:0.15, G:0.36, T:0.23
Consensus pattern (18 bp):
GAAGCGTGAGATTCGTCT
Found at i:51634 original size:14 final size:14
Alignment explanation
Indices: 51615--51707 Score: 84
Period size: 14 Copynumber: 6.6 Consensus size: 14
51605 CTCGAGTACA
51615 TATTTAATAATAAT
1 TATTTAATAATAAT
*
51629 TATTTAA-ATTTAAT
1 TATTTAATA-ATAAT
*
51643 TATTTAACT-TTAAT
1 TATTTAA-TAATAAT
*
51657 GATTTAATAATAAT
1 TATTTAATAATAAT
*
51671 TATTTAACT-TTAAT
1 TATTTAA-TAATAAT
*
51685 GATTTAATAATAAT
1 TATTTAATAATAAT
51699 TACTTTAAT
1 TA-TTTAAT
51708 GATTTAACTT
Statistics
Matches: 64, Mismatches: 8, Indels: 13
0.75 0.09 0.15
Matches are distributed among these distances:
13 3 0.05
14 54 0.84
15 7 0.11
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (14 bp):
TATTTAATAATAAT
Found at i:51662 original size:8 final size:8
Alignment explanation
Indices: 51651--52361 Score: 412
Period size: 8 Copynumber: 94.8 Consensus size: 8
51641 ATTATTTAAC
51651 TTTAATGA
1 TTTAATGA
51659 TTTAAT-A
1 TTTAATGA
* *
51666 -ATAATTA
1 TTTAATGA
*
51673 TTTAA--C
1 TTTAATGA
51679 TTTAATGA
1 TTTAATGA
51687 TTTAAT-A
1 TTTAATGA
* *
51694 -ATAATTA
1 TTTAATGA
51701 CTTTAATGA
1 -TTTAATGA
*
51710 TTTAA--C
1 TTTAATGA
51716 TTTAATGA
1 TTTAATGA
51724 TTTAAT-A
1 TTTAATGA
* *
51731 -ATAATTA
1 TTTAATGA
51738 CTTTAATGA
1 -TTTAATGA
51747 TTTAAT--
1 TTTAATGA
*
51753 TTTAGTGA
1 TTTAATGA
51761 TTTAAT-A
1 TTTAATGA
* *
51768 -ATAATTA
1 TTTAATGA
51775 CTTTAATGA
1 -TTTAATGA
51784 TTTAAT--
1 TTTAATGA
51790 TTTAATGA
1 TTTAATGA
51798 TTTAATGA
1 TTTAATGA
*
51806 TTTAA--C
1 TTTAATGA
51812 TTTAATGA
1 TTTAATGA
51820 TTTAATGA
1 TTTAATGA
*
51828 TTTAA--C
1 TTTAATGA
51834 TTTAATGA
1 TTTAATGA
51842 TTTAAT-A
1 TTTAATGA
* *
51849 -ATAATTA
1 TTTAATGA
51856 CTTTAATGA
1 -TTTAATGA
51865 TTTAATGA
1 TTTAATGA
51873 TTTAATGA
1 TTTAATGA
51881 TTTAAT-A
1 TTTAATGA
* *
51888 -ATAATTA
1 TTTAATGA
51895 TTTTAATGA
1 -TTTAATGA
51904 TTTAATGA
1 TTTAATGA
51912 TTTAAT-A
1 TTTAATGA
* *
51919 -ATAATTA
1 TTTAATGA
51926 CTTTAATGA
1 -TTTAATGA
*
51935 TTTAA--C
1 TTTAATGA
*
51941 TTTAATGC
1 TTTAATGA
51949 TTTAAT-A
1 TTTAATGA
* *
51956 -ATAATTA
1 TTTAATGA
51963 CTTTAATGA
1 -TTTAATGA
51972 TTTAATGA
1 TTTAATGA
51980 TTTAATGA
1 TTTAATGA
51988 TTTAATGA
1 TTTAATGA
51996 TTTAAT-A
1 TTTAATGA
* *
52003 -ATAATTA
1 TTTAATGA
52010 CTTTAATGA
1 -TTTAATGA
*
52019 TTTAA--C
1 TTTAATGA
52025 TTTAATGA
1 TTTAATGA
52033 TTTAAT-A
1 TTTAATGA
* *
52040 -ATAATTA
1 TTTAATGA
52047 CTTTAATGA
1 -TTTAATGA
52056 TTTAAT--
1 TTTAATGA
*
52062 TTTAATAA
1 TTTAATGA
52070 TTTAAT-A
1 TTTAATGA
* *
52077 -ATAATTA
1 TTTAATGA
52084 CTTTAATGA
1 -TTTAATGA
52093 TTTAAT--
1 TTTAATGA
*
52099 TTTAATAA
1 TTTAATGA
52107 TTTAATGA
1 TTTAATGA
52115 TTTAATGA
1 TTTAATGA
*
52123 TTTAA--C
1 TTTAATGA
52129 TTTAATGA
1 TTTAATGA
52137 TTTAAT-A
1 TTTAATGA
* *
52144 -ATAATTA
1 TTTAATGA
52151 CTTTAATGA
1 -TTTAATGA
52160 TTTAATGA
1 TTTAATGA
52168 TTTAAT-A
1 TTTAATGA
* *
52175 -ATAATTA
1 TTTAATGA
52182 TTTTAATGA
1 -TTTAATGA
52191 TTTAATGA
1 TTTAATGA
52199 TTTAAT-A
1 TTTAATGA
* *
52206 -ATAATTA
1 TTTAATGA
52213 CTTTAATGA
1 -TTTAATGA
*
52222 TTTAA--C
1 TTTAATGA
*
52228 TTTAATGC
1 TTTAATGA
52236 TTTAAT-A
1 TTTAATGA
* *
52243 -ATAATTA
1 TTTAATGA
52250 CTTTAATGA
1 -TTTAATGA
52259 TTTAATGA
1 TTTAATGA
52267 TTTAATGA
1 TTTAATGA
52275 TTTAATGA
1 TTTAATGA
52283 TTTAAT-A
1 TTTAATGA
* *
52290 -ATAATTA
1 TTTAATGA
52297 CTTTAATGA
1 -TTTAATGA
*
52306 TTTAATAA
1 TTTAATGA
52314 TTTAAT-A
1 TTTAATGA
* *
52321 -ATAATTA
1 TTTAATGA
*
52328 CTTAAT--
1 TTTAATGA
52334 TTTAATGA
1 TTTAATGA
52342 TTTAAT--
1 TTTAATGA
52348 TTTAATGA
1 TTTAATGA
52356 TTTAAT
1 TTTAAT
52362 AATAATTACT
Statistics
Matches: 556, Mismatches: 70, Indels: 154
0.71 0.09 0.20
Matches are distributed among these distances:
6 142 0.26
7 32 0.06
8 307 0.55
9 75 0.13
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.50
Consensus pattern (8 bp):
TTTAATGA
Found at i:51714 original size:37 final size:37
Alignment explanation
Indices: 51667--52280 Score: 584
Period size: 37 Copynumber: 16.7 Consensus size: 37
51657 GATTTAATAA
*
51667 TAATTATTTAACTTTAATGATTTAATAATAATTACTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
51704 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
* *
51741 TAATGATTTAATTTTAGTGATTTAATAATAATTACTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
* * *
51778 TAATGATTTAATTTTAATGATTTAATGATTTAACTTTAATGATT
1 TAATGATTTAACTTTAATGATTTAAT-A-ATAA--TT-A--CTT
51822 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
* *
51859 TAATGATTTAATGATTTAATGATTTAATAATAATTATTT
1 TAATGATTTAA--CTTTAATGATTTAATAATAATTACTT
51898 TAATG-----A-TTTAATGATTTAATAATAATTACTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
*
51929 TAATGATTTAACTTTAATGCTTTAATAATAATTACTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
* * *
51966 TAATGATTTAATGATTTAATGATTTAATGAT--TTA--A
1 TAATGATTTAA--CTTTAATGATTTAATAATAATTACTT
* * *
52001 TAAT-AATT-ACTTTAATGATTTAACT-TTAATGA-TT
1 TAATGATTTAACTTTAATGATTTAA-TAATAATTACTT
* ** *
52035 TAATAATAATT-ACTTTAATGATTTAATTTTAA-TAATT
1 TAATGAT--TTAACTTTAATGATTTAATAATAATTACTT
* *
52072 TAATAATAATT-ACTTTAATGATTTAATTTTAATAATTTAATGATT
1 TAATGAT--TTAACTTTAATGATTTAA---TAATAA-TT-A--CTT
52117 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
*
52154 TAATG-----A-TTTAATGATTTAATAATAATTATTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
52185 TAATG-----A-TTTAATGATTTAATAATAATTACTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
*
52216 TAATGATTTAACTTTAATGCTTTAATAATAATTACTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
*
52253 TAATGATTTAATGATTTAATGATTTAAT
1 TAATGATTTAA--CTTTAATGATTTAAT
52281 GATTTAATAA
Statistics
Matches: 501, Mismatches: 33, Indels: 84
0.81 0.05 0.14
Matches are distributed among these distances:
31 102 0.20
32 2 0.00
33 3 0.01
34 8 0.02
35 5 0.01
36 4 0.01
37 238 0.48
38 1 0.00
39 62 0.12
40 8 0.02
41 8 0.02
42 5 0.01
43 4 0.01
44 42 0.08
45 9 0.02
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (37 bp):
TAATGATTTAACTTTAATGATTTAATAATAATTACTT
Found at i:51953 original size:84 final size:82
Alignment explanation
Indices: 51774--52362 Score: 460
Period size: 84 Copynumber: 7.2 Consensus size: 82
51764 AATAATAATT
* * * *
51774 ACTTTAATGATTTAAT-TTTAATGATTTAATGAT-TTAACTTTAATGATTTAATGATTTAACT-T
1 ACTTTAATGATTTAATATTTAATGATTTAATAATAATGA-TTTAATGATTTAATGATTTAA-TAA
* *
51836 TAATGA-TTTAATAATAATT-
64 TAATTACTTTAATGAT--TTA
*
51855 ACTTTAATGATTTAATGATTTAATGATTTAATAATAATTATTTTAATGATTTAATGATTTAATAA
1 ACTTTAATGATTTAAT-ATTTAATGATTTAATAATAATGA-TTTAATGATTTAATGATTTAATAA
51920 TAATTACTTTAATGATTTA
64 TAATTACTTTAATGATTTA
* * * *
51939 ACTTTAATGCTTTAATA-ATAATTACTTTAATGATTTAATGATTTAATGATTTAATGATTTAATA
1 ACTTTAATGATTTAATATTTAATGA-TTTAAT-A-ATAATGATTTAATGATTTAATGATTTAATA
52003 ATAATTACTTTAATGATTTA
63 ATAATTACTTTAATGATTTA
* * * *
52023 ACTTTAATGATTT-A-A--TAAT-AATTACT-TTAATGATTTAAT--TTTAATAATTTAATAATA
1 ACTTTAATGATTTAATATTTAATGATTTAATAATAATGATTTAATGATTTAATGATTTAATAATA
52080 ATTACTTTAATGATTTA
66 ATTACTTTAATGATTTA
* * * * *
52097 ATTTTAATAATTTAATGATTTAATGATTTAACT-TTAATGATTTAAT-A-ATAATTACTTTAATG
1 ACTTTAATGATTTAAT-ATTTAATGATTTAA-TAATAATGATTTAATGATTTAATGA-TTTAAT-
* * *
52159 ATTTAATGA-TTTAATAATAATT-
62 A-ATAATTACTTTAATGAT--TTA
* * * * * *
52181 ATTTTAATGATTTAATGATTTAATAATAATTACT-TTAATGATTTAA--CTTTAATGCTTTAATA
1 ACTTTAATGATTTAAT-ATTTAATGAT--TTAATAATAATGATTTAATGATTTAATGATTTAATA
52243 ATAATTACTTTAATG-----
63 ATAATTACTTTAATGATTTA
* *
52258 A-TTTAATGATTTAATGATTTAATGATTTAATAATAATTACTTTAATGATTTAATAATTTAATAA
1 ACTTTAATGATTTAAT-ATTTAATGATTTAATAATAATGA-TTTAATGATTTAATGATTTAATAA
52322 TAATTACTTAATTTTAATGATTTA
64 TAATTAC-----TTTAATGATTTA
*
52346 ATTTTAATGATTTAATA
1 ACTTTAATGATTTAATA
52363 ATAATTACTT
Statistics
Matches: 425, Mismatches: 42, Indels: 75
0.78 0.08 0.14
Matches are distributed among these distances:
74 49 0.12
75 6 0.01
76 42 0.10
77 2 0.00
78 21 0.05
79 8 0.02
80 5 0.01
81 39 0.09
82 17 0.04
83 50 0.12
84 135 0.32
85 32 0.08
86 3 0.01
88 2 0.00
89 14 0.03
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.50
Consensus pattern (82 bp):
ACTTTAATGATTTAATATTTAATGATTTAATAATAATGATTTAATGATTTAATGATTTAATAATA
ATTACTTTAATGATTTA
Found at i:52302 original size:31 final size:31
Alignment explanation
Indices: 52267--52347 Score: 132
Period size: 31 Copynumber: 2.7 Consensus size: 31
52257 GATTTAATGA
52267 TTTAATGATTTAATGATTTAATAATAATTAC
1 TTTAATGATTTAATGATTTAATAATAATTAC
*
52298 TTTAATGATTTAATAATTTAATAATAATTAC
1 TTTAATGATTTAATGATTTAATAATAATTAC
52329 -TTAAT--TTTAATGATTTAAT
1 TTTAATGATTTAATGATTTAAT
52348 TTTAATGATT
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
28 13 0.27
30 5 0.10
31 30 0.62
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (31 bp):
TTTAATGATTTAATGATTTAATAATAATTAC
Found at i:52332 original size:14 final size:14
Alignment explanation
Indices: 52284--52372 Score: 52
Period size: 14 Copynumber: 6.1 Consensus size: 14
52274 ATTTAATGAT
52284 TTAATAATAATTAC
1 TTAATAATAATTAC
* * *
52298 TTTAATGATTTAATAAT
1 -TTAAT-A-ATAATTAC
52315 TTAATAATAATTAC
1 TTAATAATAATTAC
** * *
52329 TTAATTTTAATGAT
1 TTAATAATAATTAC
** * *
52343 TTAATTTTAATGAT
1 TTAATAATAATTAC
52357 TTAATAATAATTAC
1 TTAATAATAATTAC
52371 TT
1 TT
52373 GACTTTAATG
Statistics
Matches: 58, Mismatches: 14, Indels: 5
0.75 0.18 0.06
Matches are distributed among these distances:
14 41 0.71
15 6 0.10
16 6 0.10
17 5 0.09
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (14 bp):
TTAATAATAATTAC
Found at i:52393 original size:115 final size:113
Alignment explanation
Indices: 52152--52407 Score: 358
Period size: 115 Copynumber: 2.2 Consensus size: 113
52142 TAATAATTAC
* *
52152 TTTAATGATTTAATGATTTAATAATAATTATTTTAATGATTTAATGATTTAATAATAATTACTTT
1 TTTAATGATTTAATGATTTAATAATAATTACTTTAATGATTTAATAATTTAATAATAATTACTTT
*
52217 AATGATTTAACTTTAATGCTTTAATAATAATTACTTTAATGATTTAATGA
66 AATGATTTAACTTTAATGATTTAATAATAATTAC-TT-ATGATTTAATGA
52267 TTTAATGATTTAATGATTTAATAATAATTACTTTAATGATTTAATAATTTAATAATAATTACTTA
1 TTTAATGATTTAATGATTTAATAATAATTACTTTAATGATTTAATAATTTAATAATAATTAC---
*
52332 ATTTTAATGATTTAATTTTAATGATTTAATAATAATTAC-T-TGACTTTAATGA
63 --TTTAATGATTTAACTTTAATGATTTAATAATAATTACTTATGA-TTTAATGA
* *
52384 TTT-AT-ATTTACTGATATAATAATA
1 TTTAATGATTTAATGATTTAATAATA
52408 GTAAATATAT
Statistics
Matches: 129, Mismatches: 6, Indels: 12
0.88 0.04 0.08
Matches are distributed among these distances:
115 77 0.60
116 5 0.04
117 11 0.09
118 1 0.01
120 35 0.27
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.50
Consensus pattern (113 bp):
TTTAATGATTTAATGATTTAATAATAATTACTTTAATGATTTAATAATTTAATAATAATTACTTT
AATGATTTAACTTTAATGATTTAATAATAATTACTTATGATTTAATGA
Found at i:54590 original size:2 final size:2
Alignment explanation
Indices: 54583--54612 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
54573 AATTTATCAT
54583 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
54613 AATAGATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:56149 original size:20 final size:20
Alignment explanation
Indices: 56124--56175 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
56114 ACTGACTGAA
56124 AGTATCGATACTAGCCCAAG
1 AGTATCGATACTAGCCCAAG
56144 AGTATCGATACTAGCCCAAG
1 AGTATCGATACTAGCCCAAG
56164 AGTATCGATACT
1 AGTATCGATACT
56176 TCATATAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (20 bp):
AGTATCGATACTAGCCCAAG
Found at i:58951 original size:20 final size:20
Alignment explanation
Indices: 58926--58981 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
58916 ATATTAGCCT
58926 TACAGTATCAATACCCT-CTC
1 TACAGTATCAATACCCTAC-C
* *
58946 TACAGTATCGATACTCTACC
1 TACAGTATCAATACCCTACC
58966 TA-AGATATCAATACCC
1 TACAG-TATCAATACCC
58982 CTACAACAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 2 0.07
20 27 0.90
21 1 0.03
ACGTcount: A:0.34, C:0.30, G:0.07, T:0.29
Consensus pattern (20 bp):
TACAGTATCAATACCCTACC
Found at i:59367 original size:20 final size:20
Alignment explanation
Indices: 59329--59367 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
59319 ACGAAGAACA
* *
59329 AGTATCGATATTATCCCTAT
1 AGTATCGATACTATACCTAT
*
59349 AGTATCGATACTCTACCTA
1 AGTATCGATACTATACCTA
59368 AAGAAGTTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (20 bp):
AGTATCGATACTATACCTAT
Found at i:65890 original size:6 final size:6
Alignment explanation
Indices: 65879--65906 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
65869 AATCCGAAGG
65879 TGAATC TGAATC TGAATC TGAATC TGAA
1 TGAATC TGAATC TGAATC TGAATC TGAA
65907 ATGAAAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (6 bp):
TGAATC
Found at i:76541 original size:16 final size:16
Alignment explanation
Indices: 76512--76561 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
76502 GTATCACCGA
* *
76512 CAAAATATTTACTATT
1 CAAAAAATTCACTATT
76528 CAAAAAATTCACTATT
1 CAAAAAATTCACTATT
**
76544 CACGAAATTCACTATT
1 CAAAAAATTCACTATT
76560 CA
1 CA
76562 TGTAAATAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.44, C:0.20, G:0.02, T:0.34
Consensus pattern (16 bp):
CAAAAAATTCACTATT
Found at i:78432 original size:21 final size:21
Alignment explanation
Indices: 78406--78474 Score: 111
Period size: 21 Copynumber: 3.3 Consensus size: 21
78396 TGAATAGTGT
78406 TACAGTGTACCGATGCACTGC
1 TACAGTGTACCGATGCACTGC
* *
78427 TACAGTGTACCAATGCATTGC
1 TACAGTGTACCGATGCACTGC
*
78448 TACAGTGTACCGATGCACTGT
1 TACAGTGTACCGATGCACTGC
78469 TACAGT
1 TACAGT
78475 ACTACTACAG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.28
Consensus pattern (21 bp):
TACAGTGTACCGATGCACTGC
Found at i:79050 original size:22 final size:21
Alignment explanation
Indices: 79025--79085 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 21
79015 GGCATGTGAA
*
79025 ATTTGTCTCGAATGACCTATGT
1 ATTTGTC-CGAAGGACCTATGT
*
79047 ATTTGTCCTGAAGGACCTCTGT
1 ATTTGTCC-GAAGGACCTATGT
*
79069 ATATGTCCCGAAGGACC
1 ATTTGT-CCGAAGGACC
79086 GCGTAGACCC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.03
22 31 0.91
23 2 0.06
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (21 bp):
ATTTGTCCGAAGGACCTATGT
Found at i:81974 original size:2 final size:2
Alignment explanation
Indices: 81967--82006 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
81957 TTTACTACTA
*
81967 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
82007 GCAAACTCAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:89573 original size:20 final size:21
Alignment explanation
Indices: 89548--89586 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
89538 TTTGTAGTCG
89548 TTTCTAGCC-TTTGGGGATAA
1 TTTCTAGCCGTTTGGGGATAA
89568 TTTCTAGCCGTTTGGGGAT
1 TTTCTAGCCGTTTGGGGAT
89587 GTTTTCTCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.15, C:0.15, G:0.28, T:0.41
Consensus pattern (21 bp):
TTTCTAGCCGTTTGGGGATAA
Found at i:90600 original size:15 final size:16
Alignment explanation
Indices: 90579--90617 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
90569 AATTTAGGTC
90579 AAAAATTAAA-ATTTG
1 AAAAATTAAACATTTG
*
90594 TAAAATTAAAGCATTTG
1 AAAAATTAAA-CATTTG
90611 AAAAATT
1 AAAAATT
90618 GATATAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 9 0.45
17 11 0.55
ACGTcount: A:0.56, C:0.03, G:0.08, T:0.33
Consensus pattern (16 bp):
AAAAATTAAACATTTG
Found at i:91664 original size:3 final size:3
Alignment explanation
Indices: 91656--91814 Score: 209
Period size: 3 Copynumber: 53.7 Consensus size: 3
91646 TTTATCCATT
* *
91656 TTA TTA TTA TTA TTA TTA ATA TTA ATA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
** * * *
91704 TTA TTA GCA TT- TTA TTA TTA TTA TTA TTA ATA TTA TCA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
91751 TTA TTA TTA TTA TTA TTA -TA TTTA TTA TTA TTA -TA TTA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA T-TA TTA
91796 TTA TTA -TA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT
91815 TAATAATAAT
Statistics
Matches: 136, Mismatches: 14, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
2 8 0.06
3 123 0.90
4 5 0.04
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:92231 original size:14 final size:15
Alignment explanation
Indices: 92202--92242 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
92192 GGAGAGAGCA
*
92202 AGAAGAAAAGAAACAG
1 AGAAGAAAA-ATACAG
92218 A-AAGAAAAATACAG
1 AGAAGAAAAATACAG
92232 AGAA-AAAAATA
1 AGAAGAAAAATA
92243 ACAACAACAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 13 0.57
15 9 0.39
16 1 0.04
ACGTcount: A:0.73, C:0.05, G:0.17, T:0.05
Consensus pattern (15 bp):
AGAAGAAAAATACAG
Found at i:104425 original size:1 final size:1
Alignment explanation
Indices: 104419--104499 Score: 63
Period size: 1 Copynumber: 81.0 Consensus size: 1
104409 CTTGAAGAAG
* * * * * * * * *
104419 AAAAAAAGAGAAAAAAGAAAAAGAAAAAAAAAGAAAAAGAAAAAAAAAATAAAAGAAAAAAAAAG
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
104484 GAAAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAA
104500 GAGGGTCAAG
Statistics
Matches: 60, Mismatches: 20, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 60 1.00
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.01
Consensus pattern (1 bp):
A
Found at i:104448 original size:16 final size:16
Alignment explanation
Indices: 104416--104501 Score: 106
Period size: 16 Copynumber: 5.2 Consensus size: 16
104406 ATGCTTGAAG
104416 AAGAAAAA-AAGAGAAAA
1 AAGAAAAAGAA-A-AAAA
104433 AAGAAAAAGAAAAAAA
1 AAGAAAAAGAAAAAAA
104449 AAGAAAAAGAAAAAAA
1 AAGAAAAAGAAAAAAA
104465 AA-ATAAAAGAAAAAAA
1 AAGA-AAAAGAAAAAAA
104481 AAGGAAAAA-AAGAAAAA
1 AA-GAAAAAGAA-AAAAA
104498 AAGA
1 AAGA
104502 GGGTCAAGGT
Statistics
Matches: 64, Mismatches: 0, Indels: 11
0.85 0.00 0.15
Matches are distributed among these distances:
15 1 0.02
16 40 0.62
17 20 0.31
18 3 0.05
ACGTcount: A:0.85, C:0.00, G:0.14, T:0.01
Consensus pattern (16 bp):
AAGAAAAAGAAAAAAA
Found at i:104465 original size:32 final size:33
Alignment explanation
Indices: 104416--104501 Score: 124
Period size: 32 Copynumber: 2.6 Consensus size: 33
104406 ATGCTTGAAG
104416 AAGAAAAAAAGAGAAAAAAGA-AAAAGAAAAAAA
1 AAGAAAAAAAGA-AAAAAAGATAAAAGAAAAAAA
104449 AAGAAAAAGAA-AAAAAAA-ATAAAAGAAAAAAA
1 AAGAAAAA-AAGAAAAAAAGATAAAAGAAAAAAA
104481 AAGGAAAAAAAGAAAAAAAGA
1 AA-GAAAAAAAGAAAAAAAGA
104502 GGGTCAAGGT
Statistics
Matches: 48, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
31 1 0.02
32 22 0.46
33 22 0.46
34 3 0.06
ACGTcount: A:0.85, C:0.00, G:0.14, T:0.01
Consensus pattern (33 bp):
AAGAAAAAAAGAAAAAAAGATAAAAGAAAAAAA
Found at i:105749 original size:102 final size:102
Alignment explanation
Indices: 105614--106008 Score: 722
Period size: 102 Copynumber: 3.9 Consensus size: 102
105604 GACTCAATAA
105614 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAACATAGCATCTTCTGGAAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACATAGCATCTTCTGGAAG
*
105678 TGTTCTTTGAGTTATCTGATCTGTTTAGAAGAACATAG
66 TGTTCTTTGAGTTATCTGATCTGGTT-GAAGAACATAG
105716 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAACATAGCATCTTCTGGAAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACATAGCATCTTCTGGAAG
105780 TGTTCTTTGAGTTATCTGATCTGGTTGAAGAACATAG
66 TGTTCTTTGAGTTATCTGATCTGGTTGAAGAACATAG
105817 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACATAGCATCTTCTGGAAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACATAGCATCTTCTGGAAG
*
105882 TGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAA
66 TGTTCTTTGAGTTATCTGATCTGGTT-GA-AGAACATAG
*
105921 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTGGAAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACATAGCATCTTCTGGAAG
105986 TGTTCTTTGAGTTATCTGATCTG
66 TGTTCTTTGAGTTATCTGATCTG
106009 ATTGGACAGA
Statistics
Matches: 287, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
101 53 0.18
102 137 0.48
103 2 0.01
104 95 0.33
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.38
Consensus pattern (102 bp):
CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACATAGCATCTTCTGGAAG
TGTTCTTTGAGTTATCTGATCTGGTTGAAGAACATAG
Found at i:106027 original size:52 final size:51
Alignment explanation
Indices: 105614--106008 Score: 720
Period size: 52 Copynumber: 7.7 Consensus size: 51
105604 GACTCAATAA
105614 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
*
105665 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTAGAAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
105716 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
105767 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GAAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
105817 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAACATAG
* *
105869 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAA
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAACATAG
*
105921 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAACATAG
105973 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
106009 ATTGGACAGA
Statistics
Matches: 337, Mismatches: 5, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
50 50 0.15
51 141 0.42
52 146 0.43
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.38
Consensus pattern (51 bp):
CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
Found at i:106841 original size:113 final size:113
Alignment explanation
Indices: 106643--107204 Score: 905
Period size: 113 Copynumber: 5.0 Consensus size: 113
106633 TTTAGCAAAG
106643 ACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT
1 ACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT
106708 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
66 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
* * *
106756 ACCTGAATCCATCATTTGGTGGATCATCATTACCAGAGAAGGTTCATAATGAGAAGAACTCATCT
1 ACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT
106821 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
66 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
106869 ACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT
1 ACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT
106934 GAAGAA-G--GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
66 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
106979 ACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT
1 ACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT
* * * *
107044 AAATAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTT
66 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
*** * * * * * ** * *
107092 GTTTAAATTCATCATTTGATGGATCAACATGGCCAAAGAAAGTTCATGAATAAGAAGAACTCATC
1 ACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCAT-AATGAGAAGAACTCATC
**
107157 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTT
65 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTT
107205 GTTTGATATC
Statistics
Matches: 419, Mismatches: 26, Indels: 7
0.93 0.06 0.02
Matches are distributed among these distances:
110 107 0.26
111 1 0.00
112 1 0.00
113 250 0.60
114 60 0.14
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (113 bp):
ACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT
GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
Found at i:107034 original size:223 final size:225
Alignment explanation
Indices: 106643--107204 Score: 894
Period size: 223 Copynumber: 2.5 Consensus size: 225
106633 TTTAGCAAAG
106643 ACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT
1 ACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT
106708 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTT
66 GAAGAAGG-AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTT
* *
106773 GGTGGATCATCATTACCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
130 GGTGGATCATCATTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAG
*
106838 TTCATAATGAGAAGAATTTGTTCAACCTTTT
195 TTCATAATGAGAAGAACTTGTTCAACCTTTT
106869 ACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT
1 ACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT
106934 GAAGAA-G-GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTG
66 GAAGAAGGAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTG
* * *
106997 GTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTAAATAAGGAAGAAGAAGT
131 GTGGATCATCATTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAGT
*
107062 TCATAATGAGAAGAACTTGTTCAACTTTTT
196 TCATAATGAGAAGAACTTGTTCAACCTTTT
*** * * * * * ** * *
107092 GTTTAAATTCATCATTTGATGGATCAACATGGCCAAAGAAAGTTCATGAATAAGAAGAACTCATC
1 ACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCAT-AATGAGAAGAACTCATC
**
107157 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTT
65 TGAAGAAGG-AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTT
107205 GTTTGATATC
Statistics
Matches: 311, Mismatches: 21, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
223 180 0.58
224 23 0.07
225 2 0.01
226 71 0.23
227 35 0.11
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (225 bp):
ACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT
GAAGAAGGAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTG
GTGGATCATCATTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAGT
TCATAATGAGAAGAACTTGTTCAACCTTTT
Found at i:107509 original size:3 final size:3
Alignment explanation
Indices: 107501--107690 Score: 256
Period size: 3 Copynumber: 62.7 Consensus size: 3
107491 TTTATCCATT
* *
107501 TTA TTA TTA TTA TTA TTA ATA TTA ATA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* ** *
107549 TTA GTA TTA TTA TTA TTA TTA GCA TT- TTA TTA TTA TTA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
107596 TTA TTA TTA TCA TTA TTA ATA TTA TTA TTA TTA TTA TTA TTA GTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
*
107645 TTA TTA TTA TTA ATA TTA TATA TTA TTA TTA TATA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA T-TA TTA TTA TTA TT
107691 TAATAAATAA
Statistics
Matches: 163, Mismatches: 20, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
2 2 0.01
3 153 0.94
4 8 0.05
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:113277 original size:29 final size:27
Alignment explanation
Indices: 113228--113300 Score: 69
Period size: 29 Copynumber: 2.6 Consensus size: 27
113218 TTAACTTATT
113228 AAATATATTTTACTATTTTTAAC-CTAA
1 AAATATATTTTACTATTTTTAACTC-AA
* *
113255 TAATATATTTTATTCCTA-TTTTAATTCAA
1 AAATATATTTTA---CTATTTTTAACTCAA
*
113284 AAATATATTTTAATATT
1 AAATATATTTTACTATT
113301 ATCTTAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
26 2 0.05
27 12 0.32
29 19 0.51
30 4 0.11
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (27 bp):
AAATATATTTTACTATTTTTAACTCAA
Found at i:113307 original size:29 final size:29
Alignment explanation
Indices: 113256--113359 Score: 91
Period size: 31 Copynumber: 3.4 Consensus size: 29
113246 TTAACCTAAT
** * *
113256 AATATATTTTATTCCTATTTTAATTCAAA
1 AATATATTTTATTATTATCTTAATTAAAA
*
113285 AATATATTTTAATATTATCTTAAATTAAAA
1 AATATATTTTATTATTATCTT-AATTAAAA
* *
113315 AATTATAATTTCTTATTATCTTAACTTAAATA
1 AA-TATATTTTATTATTATCTTAA-TTAAA-A
**
113347 TTTATATTTTATT
1 AATATATTTTATT
113360 TTAATAATAT
Statistics
Matches: 59, Mismatches: 12, Indels: 6
0.77 0.16 0.08
Matches are distributed among these distances:
29 17 0.29
30 11 0.19
31 30 0.51
32 1 0.02
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (29 bp):
AATATATTTTATTATTATCTTAATTAAAA
Found at i:113417 original size:29 final size:29
Alignment explanation
Indices: 113380--113497 Score: 104
Period size: 29 Copynumber: 4.2 Consensus size: 29
113370 TTTAAATTTG
**
113380 AGATAAAAATGTAATATATTTTTGTAGTTA
1 AGATAAAAATAAAATATA-TTTTGTAGTTA
113410 AGATAAAAATAAAATATATTTTGTAGTTA
1 AGATAAAAATAAAATATATTTTGTAGTTA
* *
113439 AAATAAAAAT---ATAT-TTTT-AAGTTA
1 AGATAAAAATAAAATATATTTTGTAGTTA
* * *
113463 AAATAAGAATAAAAGATATTTT-TACGTTA
1 AGATAAAAATAAAATATATTTTGTA-GTTA
*
113492 AAATAA
1 AGATAA
113498 GAATTAATTA
Statistics
Matches: 76, Mismatches: 7, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
24 14 0.18
25 4 0.05
26 4 0.05
27 3 0.04
28 5 0.07
29 30 0.39
30 16 0.21
ACGTcount: A:0.52, C:0.01, G:0.09, T:0.38
Consensus pattern (29 bp):
AGATAAAAATAAAATATATTTTGTAGTTA
Found at i:113441 original size:23 final size:23
Alignment explanation
Indices: 113415--113473 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 23
113405 AGTTAAGATA
113415 AAAATAAAATATATTTTGT-AGTT
1 AAAATAAAATATATTTT-TAAGTT
113438 AAAATAAAAATATATTTTTAAGTT
1 AAAAT-AAAATATATTTTTAAGTT
113462 AAAATAAGAATA
1 AAAATAA-AATA
113474 AAAGATATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
23 8 0.24
24 25 0.76
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (23 bp):
AAAATAAAATATATTTTTAAGTT
Found at i:113474 original size:53 final size:54
Alignment explanation
Indices: 113392--113497 Score: 153
Period size: 53 Copynumber: 2.0 Consensus size: 54
113382 ATAAAAATGT
* * *
113392 AATATATTTTTGTAGTTAAGATAAAAATAAAATATATTTTGTA-GTTAAAATAAA
1 AATATATTTTTGAAGTTAAAATAAAAATAAAAGATATTTT-TACGTTAAAATAAA
*
113446 AATATATTTTT-AAGTTAAAATAAGAATAAAAGATATTTTTACGTTAAAATAA
1 AATATATTTTTGAAGTTAAAATAAAAATAAAAGATATTTTTACGTTAAAATAA
113498 GAATTAATTA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
52 2 0.04
53 34 0.72
54 11 0.23
ACGTcount: A:0.51, C:0.01, G:0.08, T:0.40
Consensus pattern (54 bp):
AATATATTTTTGAAGTTAAAATAAAAATAAAAGATATTTTTACGTTAAAATAAA
Found at i:114099 original size:44 final size:43
Alignment explanation
Indices: 114047--114274 Score: 117
Period size: 41 Copynumber: 5.4 Consensus size: 43
114037 GCTAAAACTC
114047 GTACTTTAGTGGCGTTTTTATGACAAACGCTCTGCTAAAGATAA
1 GTACTTTAGTGGCGTTTTTA-GACAAACGCTCTGCTAAAGATAA
* * * * * *
114091 GTACTTTAGCGGTGTTTGTAAACAAA--CACTGC-AATATGGTACA
1 GTACTTTAGTGGCGTTTTTAGACAAACGCTCTGCTAA-A-GATA-A
* *
114134 -TA-TATTA-TGGCGTTTTTAGACAAACG-TC-GCTAAAAATTA
1 GTACT-TTAGTGGCGTTTTTAGACAAACGCTCTGCTAAAGATAA
* * * * * *
114173 GTACTTTAGTGGCGTTTTAAGCAAAAATGC-C-GTTAAATACT-C
1 GTACTTTAGTGGCGTTTTTAG-ACAAACGCTCTGCTAAAGA-TAA
* *
114215 GTACTTTAGTGGCATTTTTAGACAAACG-TC-GTTAAA-ACCT-A
1 GTACTTTAGTGGCGTTTTTAGACAAACGCTCTGCTAAAGA--TAA
*
114256 GTACTTTAGTGGCCTTTTT
1 GTACTTTAGTGGCGTTTTT
114275 TTGACAAATG
Statistics
Matches: 143, Mismatches: 26, Indels: 33
0.71 0.13 0.16
Matches are distributed among these distances:
39 1 0.01
40 9 0.06
41 67 0.47
42 42 0.29
43 7 0.05
44 17 0.12
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (43 bp):
GTACTTTAGTGGCGTTTTTAGACAAACGCTCTGCTAAAGATAA
Found at i:114223 original size:42 final size:41
Alignment explanation
Indices: 114141--114357 Score: 157
Period size: 42 Copynumber: 5.2 Consensus size: 41
114131 ACATATATTA
* * * * * *
114141 TGGCGTTTTTAGACAAACGTCGCTAAAAATTAGTACTTTAG
1 TGGCGTTTTAAGAAAAACGCCGCTAAATACTCGTACTTTAG
* *
114182 TGGCGTTTTAAGCAAAAATGCCGTTAAATACTCGTACTTTAG
1 TGGCGTTTTAAG-AAAAACGCCGCTAAATACTCGTACTTTAG
* * * * * *
114224 TGGCATTTTTAGACAAACGTCGTTAAA-ACCTAGTACTTTAG
1 TGGCGTTTTAAGAAAAACGCCGCTAAATA-CTCGTACTTTAG
* ** * * * *
114265 TGGCCTTTTTTTGACAAATGTCGCTAAATACTCGTATTTTAG
1 TGG-CGTTTTAAGAAAAACGCCGCTAAATACTCGTACTTTAG
* * * * *
114307 TGACGTTTTAAGCAAAAACACTGCTAAATACTCATACGTTAG
1 TGGCGTTTTAAG-AAAAACGCCGCTAAATACTCGTACTTTAG
114349 TGGCGTTTT
1 TGGCGTTTT
114358 TTATTTACAA
Statistics
Matches: 138, Mismatches: 33, Indels: 9
0.77 0.18 0.05
Matches are distributed among these distances:
40 1 0.01
41 43 0.31
42 93 0.67
43 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (41 bp):
TGGCGTTTTAAGAAAAACGCCGCTAAATACTCGTACTTTAG
Found at i:114244 original size:83 final size:83
Alignment explanation
Indices: 114141--114308 Score: 221
Period size: 83 Copynumber: 2.0 Consensus size: 83
114131 ACATATATTA
* *
114141 TGGCGTTTTTAGACAAACGTCGCTAAAAATTAGTACTTTAGTGG-CGTTTTAAGCAAAAATGCCG
1 TGGCATTTTTAGACAAACGTCGCTAAAAACTAGTACTTTAGTGGCCGTTTTAAG-AAAAATGCCG
*
114205 TTAAATACTCGTACTTTAG
65 CTAAATACTCGTACTTTAG
* * * ** * *
114224 TGGCATTTTTAGACAAACGTCGTTAAAACCTAGTACTTTAGTGGCCTTTTTTTGACAAATGTCGC
1 TGGCATTTTTAGACAAACGTCGCTAAAAACTAGTACTTTAGTGGCCGTTTTAAGAAAAATGCCGC
*
114289 TAAATACTCGTATTTTAG
66 TAAATACTCGTACTTTAG
114307 TG
1 TG
114309 ACGTTTTAAG
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
83 67 0.92
84 6 0.08
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.36
Consensus pattern (83 bp):
TGGCATTTTTAGACAAACGTCGCTAAAAACTAGTACTTTAGTGGCCGTTTTAAGAAAAATGCCGC
TAAATACTCGTACTTTAG
Found at i:118526 original size:43 final size:43
Alignment explanation
Indices: 118470--118649 Score: 254
Period size: 43 Copynumber: 4.2 Consensus size: 43
118460 TGCATATATA
* * *
118470 GCGGCTTTTGTATCCAAAAATGCAGCTATAGAGCTGACCTTTT
1 GCGGCGTTTGTATCCAAAAATGCCGCTATAGATCTGACCTTTT
* * *
118513 GTGGCGTTTGTATCAAAAAACGCCGCTATAGATCTGACCTTTT
1 GCGGCGTTTGTATCCAAAAATGCCGCTATAGATCTGACCTTTT
* **
118556 GCGACGTTTGT-TCCAAAAATATCGCTATAGATCTGACCTTTT
1 GCGGCGTTTGTATCCAAAAATGCCGCTATAGATCTGACCTTTT
* *
118598 GCGGCGTTTGTATCCAAAAATGCCGTTATAGATCTGACCTTTA
1 GCGGCGTTTGTATCCAAAAATGCCGCTATAGATCTGACCTTTT
118641 GCGGCGTTT
1 GCGGCGTTT
118650 ATTCTAAAAA
Statistics
Matches: 119, Mismatches: 17, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
42 37 0.31
43 82 0.69
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.33
Consensus pattern (43 bp):
GCGGCGTTTGTATCCAAAAATGCCGCTATAGATCTGACCTTTT
Found at i:118583 original size:85 final size:85
Alignment explanation
Indices: 118476--118661 Score: 257
Period size: 85 Copynumber: 2.2 Consensus size: 85
118466 TATAGCGGCT
*
118476 TTTGTATCCAAAAATGCAGCTATAGAGCTGACCTTTTGTGGCGTTTGTATCAAAAAACGCCGCTA
1 TTTGT-TCCAAAAATGCAGCTATAGAGCTGACCTTTTGCGGCGTTTGTATCAAAAAACGCCGCTA
*
118541 TAGATCTGACCTTTTGCGACG
65 TAGATCTGACCTTTAGCGACG
* * * * *
118562 TTTGTTCCAAAAATATC-GCTATAGATCTGACCTTTTGCGGCGTTTGTATCCAAAAATGCCGTTA
1 TTTGTTCCAAAAAT-GCAGCTATAGAGCTGACCTTTTGCGGCGTTTGTATCAAAAAACGCCGCTA
*
118626 TAGATCTGACCTTTAGCGGCG
65 TAGATCTGACCTTTAGCGACG
* *
118647 TTTATTCTAAAAATG
1 TTTGTTCCAAAAATG
118662 TTGTTATATA
Statistics
Matches: 88, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
85 82 0.93
86 6 0.07
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (85 bp):
TTTGTTCCAAAAATGCAGCTATAGAGCTGACCTTTTGCGGCGTTTGTATCAAAAAACGCCGCTAT
AGATCTGACCTTTAGCGACG
Found at i:118680 original size:43 final size:44
Alignment explanation
Indices: 118468--118682 Score: 118
Period size: 43 Copynumber: 5.0 Consensus size: 44
118458 AATGCATATA
* * * * * **
118468 TAGCGGCTTTTGTATCCAAAAATGCAGCTATAGAGCT-GACCTT
1 TAGCGGCGTTTATATCCAAAAATGCCGTTATATATATCGACCTT
* * * * * * * *
118511 TTGTGGCGTTTGTATCAAAAAACGCCGCTATAGATCT-GACCTT
1 TAGCGGCGTTTATATCCAAAAATGCCGTTATATATATCGACCTT
* * * ** * * *
118554 TTGCGACGTTTGT-TCCAAAAATATCGCTATAGATCT-GACCTT
1 TAGCGGCGTTTATATCCAAAAATGCCGTTATATATATCGACCTT
* * * *
118596 TTGCGGCGTTTGTATCCAAAAATGCCGTTATAGATCT-GACCTT
1 TAGCGGCGTTTATATCCAAAAATGCCGTTATATATATCGACCTT
* **
118639 TAGCGGCGTTTAT-TCTAAAAATGTTGTTATATATATCGACCTT
1 TAGCGGCGTTTATATCCAAAAATGCCGTTATATATATCGACCTT
118682 T
1 T
118683 TATGATGTTT
Statistics
Matches: 146, Mismatches: 24, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
42 55 0.38
43 91 0.62
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (44 bp):
TAGCGGCGTTTATATCCAAAAATGCCGTTATATATATCGACCTT
Found at i:118698 original size:128 final size:129
Alignment explanation
Indices: 118470--118723 Score: 296
Period size: 128 Copynumber: 2.0 Consensus size: 129
118460 TGCATATATA
* * * *
118470 GCGGCTTTTGTATCCAAAAATGCAGCTATAGAGCTGACCTTTTGTGGCGTTTGTATCAAAAAACG
1 GCGGCGTTTGTATCCAAAAATGCAGCTATAGAGCTGACCTTTAGCGGCGTTTATATCAAAAAACG
* * * * * *
118535 CCGCTATAGATCTGACCTTTTGCGACGTTTGTTCCAAAAATATCGCTATAGATC-TGACCTTTT
66 CCGCTATAGATATGACCTTTTACGACGTTTATTCCAAAAACACCGCGATAGATCTTGACCTTTT
* * * * *
118598 GCGGCGTTTGTATCCAAAAATGCCGTTATAGATCTGACCTTTAGCGGCGTTTAT-TCTAAAAATG
1 GCGGCGTTTGTATCCAAAAATGCAGCTATAGAGCTGACCTTTAGCGGCGTTTATATCAAAAAACG
** * * * *
118662 TTGTTATATATATCGACCTTTTATGATGTTTATTCCAAAAACACCGCGATAGATCTTGACCT
66 CCGCTATAGATAT-GACCTTTTACGACGTTTATTCCAAAAACACCGCGATAGATCTTGACCT
118724 ATTTTGGTGT
Statistics
Matches: 103, Mismatches: 21, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
127 16 0.16
128 81 0.79
129 6 0.06
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.35
Consensus pattern (129 bp):
GCGGCGTTTGTATCCAAAAATGCAGCTATAGAGCTGACCTTTAGCGGCGTTTATATCAAAAAACG
CCGCTATAGATATGACCTTTTACGACGTTTATTCCAAAAACACCGCGATAGATCTTGACCTTTT
Found at i:118699 original size:85 final size:85
Alignment explanation
Indices: 118494--118723 Score: 210
Period size: 85 Copynumber: 2.7 Consensus size: 85
118484 CAAAAATGCA
** ** * * * *
118494 GCTATAGAGCTGACCTTTTGTGGCGTTTGTATCAAAAAACGCCGCTATAGATCTGACCTTTTGCG
1 GCTATAGATATGACCTTTTACGACGTTTATATCCAAAAACGCCGCTATAGATCTGACCTTTAGCG
*
118559 ACGTTTGTTCCAAAAATATC
66 ACGTTTATTCCAAAAATATC
* * * * * *
118579 GCTATAGATCTGACCTTTTGCGGCGTTTGTATCCAAAAATGCCGTTATAGATCTGACCTTTAGCG
1 GCTATAGATATGACCTTTTACGACGTTTATATCCAAAAACGCCGCTATAGATCTGACCTTTAGCG
* * * *
118644 GCGTTTATTCTAAAAATGTT
66 ACGTTTATTCCAAAAATATC
* * * * * *
118664 GTTATATATATCGACCTTTTATGATGTTTAT-TCCAAAAACACCGCGATAGATCTTGACCT
1 GCTATAGATAT-GACCTTTTACGACGTTTATATCCAAAAACGCCGCTATAGATC-TGACCT
118724 ATTTTGGTGT
Statistics
Matches: 120, Mismatches: 23, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
85 100 0.83
86 20 0.17
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (85 bp):
GCTATAGATATGACCTTTTACGACGTTTATATCCAAAAACGCCGCTATAGATCTGACCTTTAGCG
ACGTTTATTCCAAAAATATC
Found at i:120824 original size:20 final size:22
Alignment explanation
Indices: 120799--120838 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
120789 AGTCATATCT
120799 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
120819 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
120839 TCTACAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:121083 original size:20 final size:20
Alignment explanation
Indices: 121024--121085 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
121014 GGGGTGTGGA
*
121024 TACACTGCAGGGTGTATCGG
1 TACACTGCAGAGTGTATCGG
*
121044 TACAC--C--AGTGTAT-GTA
1 TACACTGCAGAGTGTATCG-G
121060 TACACTGCAGAGTGTATCGG
1 TACACTGCAGAGTGTATCGG
121080 TACACT
1 TACACT
121086 TTAGCATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 12
0.69 0.06 0.25
Matches are distributed among these distances:
15 1 0.03
16 11 0.33
18 2 0.06
20 18 0.55
21 1 0.03
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (20 bp):
TACACTGCAGAGTGTATCGG
Found at i:127469 original size:30 final size:30
Alignment explanation
Indices: 127434--127493 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
127424 ATTATACTTA
127434 ATTATGGCTTAAAGA-AAGTTGTGTGAAATT
1 ATTAT-GCTTAAAGATAAGTTGTGTGAAATT
* * *
127464 ATTATGTTTTAGGATAAGTTGTGTGAAATT
1 ATTATGCTTAAAGATAAGTTGTGTGAAATT
127494 TAAAAAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 6 0.23
30 20 0.77
ACGTcount: A:0.33, C:0.02, G:0.23, T:0.42
Consensus pattern (30 bp):
ATTATGCTTAAAGATAAGTTGTGTGAAATT
Found at i:132925 original size:54 final size:54
Alignment explanation
Indices: 132861--132978 Score: 155
Period size: 54 Copynumber: 2.2 Consensus size: 54
132851 AATGGTGTAT
* * * **
132861 TTTCGACACTATATGTGTAAACCATGGTATTTATAATGTGTTTATGAATTACCA
1 TTTCGACACTATATGTGCAAACCATGGAATTCATAATAAGTTTATGAATTACCA
* * * *
132915 TTTCGACACTATGTGTGCAATCCATGGAATTCATAATAAGTTTGTGAATTTCCA
1 TTTCGACACTATATGTGCAAACCATGGAATTCATAATAAGTTTATGAATTACCA
132969 TTTCGACACT
1 TTTCGACACT
132979 TCGGTGCAAT
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (54 bp):
TTTCGACACTATATGTGCAAACCATGGAATTCATAATAAGTTTATGAATTACCA
Found at i:135588 original size:28 final size:28
Alignment explanation
Indices: 135526--135607 Score: 98
Period size: 28 Copynumber: 3.0 Consensus size: 28
135516 TTTCAAAAAA
*
135526 AATAAGTT-AGATAAAAATAAATATATTT
1 AATAAGTTAAAATAAAAATAAA-ATATTT
* *
135554 --TAGGTTAAAATAATAATAAAATATTT
1 AATAAGTTAAAATAAAAATAAAATATTT
*
135580 AATAAGTTAATATAAAAATAAAATATTT
1 AATAAGTTAAAATAAAAATAAAATATTT
135608 TTAATGCTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
26 11 0.24
27 11 0.24
28 23 0.51
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (28 bp):
AATAAGTTAAAATAAAAATAAAATATTT
Found at i:136420 original size:318 final size:318
Alignment explanation
Indices: 135843--136475 Score: 982
Period size: 318 Copynumber: 2.0 Consensus size: 318
135833 AAGTAACACA
* *
135843 TGTCACCCTCTAATCGGTGAGAAAAATATATTAAATTAAAAATAAATTGTGACACATGTCATTAT
1 TGTCACCCTCTAATCGGTGAGAAAAATATATTAAATTAAAAATAAATTGTAACACATATCATTAT
* * * * *
135908 ACTTGGAACCATTGATTTAAGAGTTAAGTTTATTTTAATTTATTAAAATTAGGAGCAAATTGATA
66 ACTTGGAACAATTGATTTAAGAGTTAAATTAATTTTAACTTATTAAAATTAGGACCAAATTGATA
* * * *
135973 GAATATATAAGTTACAGTGACCAAATGTTTAATTATACCAAATATTTTAATTGCCACATTAGCTT
131 GAATATATAAGTTACAGTGAACAAATGTGTAATTATACCAAATATTTTAACTGCCACATCAGCTT
* * * *
136038 CTTCGTTAAATATTAATGGCAAATGACTTAATTGAATGCATTTAAATAGTTAAGTGACTTGATTG
196 CTTCATTAAATATTAATGACAAATGACTTAATTAAATGCATTTAAATAGTTAAGAGACTTGATTG
*
136103 ACAAAATTTCAAAAATAATGGTCAAAATAAAAAGGGACAATAGTTAGGTGGTCACTGG
261 ACAAAATTTCAAAAATAATGGACAAAATAAAAAGGGACAATAGTTAGGTGGTCACTGG
* * *
136161 TGTCACCCTCTGATTGGTGAGAAAAATATATTAAATTAAAAATAAATTGTAATACATATCATTAT
1 TGTCACCCTCTAATCGGTGAGAAAAATATATTAAATTAAAAATAAATTGTAACACATATCATTAT
* * **
136226 ACTTGGCACAATTTGATTT-AGGGTTAAATTAATTTTAACTTATTAAAATTATTACCAAATTGAT
66 ACTTGGAACAA-TTGATTTAAGAGTTAAATTAATTTTAACTTATTAAAATTAGGACCAAATTGAT
*
136290 AGAATATATAAGTTACAGTGAACAAATGTGTAATTATACCAAATATTTTAACTGTCACATCAGCT
130 AGAATATATAAGTTACAGTGAACAAATGTGTAATTATACCAAATATTTTAACTGCCACATCAGCT
* *
136355 TC-TCTATTAAATATTAATGACAAGTGACTTAATTAAATGCATTTAAATAGTTGAGAGACTTGAT
195 TCTTC-ATTAAATATTAATGACAAATGACTTAATTAAATGCATTTAAATAGTTAAGAGACTTGAT
* *
136419 TGACAAAATTTCAAAAATAGTGGACAAAATGAAAAGGGACAATAGTTAGGTGGTCAC
259 TGACAAAATTTCAAAAATAATGGACAAAATAAAAAGGGACAATAGTTAGGTGGTCAC
136476 CAGTATAATT
Statistics
Matches: 285, Mismatches: 28, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
317 2 0.01
318 276 0.97
319 7 0.02
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.34
Consensus pattern (318 bp):
TGTCACCCTCTAATCGGTGAGAAAAATATATTAAATTAAAAATAAATTGTAACACATATCATTAT
ACTTGGAACAATTGATTTAAGAGTTAAATTAATTTTAACTTATTAAAATTAGGACCAAATTGATA
GAATATATAAGTTACAGTGAACAAATGTGTAATTATACCAAATATTTTAACTGCCACATCAGCTT
CTTCATTAAATATTAATGACAAATGACTTAATTAAATGCATTTAAATAGTTAAGAGACTTGATTG
ACAAAATTTCAAAAATAATGGACAAAATAAAAAGGGACAATAGTTAGGTGGTCACTGG
Found at i:136767 original size:20 final size:21
Alignment explanation
Indices: 136742--136780 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
136732 AATTAGTTAA
136742 AAAATAAA-AATAAATTATTT
1 AAAATAAACAATAAATTATTT
*
136762 AAAATAAACGATAAATTAT
1 AAAATAAACAATAAATTAT
136781 ACCAGTGACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (21 bp):
AAAATAAACAATAAATTATTT
Found at i:138339 original size:39 final size:36
Alignment explanation
Indices: 138269--138342 Score: 103
Period size: 39 Copynumber: 2.0 Consensus size: 36
138259 AACTGAAATT
* *
138269 TGTCCCTAAGGACCACTATGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTATGTCCCAAAGGACCACTA
138305 TGTCCCGAAGGACCACTGATATGTCCCAAAGGACCACT
1 TGTCCCGAAGGACCAC---TATGTCCCAAAGGACCACT
138343 GATAATCCCT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
36 15 0.45
39 18 0.55
ACGTcount: A:0.28, C:0.32, G:0.20, T:0.19
Consensus pattern (36 bp):
TGTCCCGAAGGACCACTATGTCCCAAAGGACCACTA
Found at i:138346 original size:21 final size:18
Alignment explanation
Indices: 138269--138342 Score: 103
Period size: 18 Copynumber: 3.9 Consensus size: 18
138259 AACTGAAATT
*
138269 TGTCCCTAAGGACCACTA
1 TGTCCCGAAGGACCACTA
138287 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
138305 TGTCCCGAAGGACCACTGATA
1 TGTCCCGAAGGACCAC---TA
*
138326 TGTCCCAAAGGACCACT
1 TGTCCCGAAGGACCACT
138343 GATAATCCCT
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
18 34 0.67
21 17 0.33
ACGTcount: A:0.28, C:0.32, G:0.20, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:142017 original size:17 final size:17
Alignment explanation
Indices: 141995--142029 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
141985 TATCCTGACA
*
141995 ATATCTTATAATCTTAT
1 ATATCTTATAATCCTAT
142012 ATATCTTATAATCCTAT
1 ATATCTTATAATCCTAT
142029 A
1 A
142030 CTTCCAGTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (17 bp):
ATATCTTATAATCCTAT
Done.