Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012203.1 Corchorus olitorius cultivar O-4 contig12236, 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: 87712
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:929 original size:109 final size:109
Alignment explanation
Indices: 733--954 Score: 399
Period size: 109 Copynumber: 2.0 Consensus size: 109
723 AGGAGGGAAT
733 TTAATAAACTACTCCGCTGTTTTTGGGAAGTGGAGCACACGGGGTTCGGTATCACAAATATCAAC
1 TTAATAAACTACTCCGCTGTTTTTGGGAAGTGGAGCACACGGGGTTCGGTATCACAAATATCAAC
*
798 CTTCGCGTCAGTCACGAACCAAAATTATGAGTATGCAAAGCATC
66 CTTCGCGTCAGTCACGAACCAAAATTATGAGTATGCAAAGCACC
* *
842 TTAATAAACTACTCCTCTGTTTTTTGGAAGTGGAGCACACGGGGTTCGGTATCACAAATATCAAC
1 TTAATAAACTACTCCGCTGTTTTTGGGAAGTGGAGCACACGGGGTTCGGTATCACAAATATCAAC
* *
907 CTTCGCGTCAGTCACGACCCAAAATTATGAGTATGCAAGGCACC
66 CTTCGCGTCAGTCACGAACCAAAATTATGAGTATGCAAAGCACC
951 TTAA
1 TTAA
955 ATGCGTAAGT
Statistics
Matches: 108, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
109 108 1.00
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.27
Consensus pattern (109 bp):
TTAATAAACTACTCCGCTGTTTTTGGGAAGTGGAGCACACGGGGTTCGGTATCACAAATATCAAC
CTTCGCGTCAGTCACGAACCAAAATTATGAGTATGCAAAGCACC
Found at i:1767 original size:21 final size:21
Alignment explanation
Indices: 1742--1781 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1732 ATTGGATATA
*
1742 TGAAACTCCAAGGTTTCAATT
1 TGAAACCCCAAGGTTTCAATT
1763 TGAAACCCCAAGGTTTCAA
1 TGAAACCCCAAGGTTTCAA
1782 GCTTTTGCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.28
Consensus pattern (21 bp):
TGAAACCCCAAGGTTTCAATT
Found at i:3584 original size:19 final size:18
Alignment explanation
Indices: 3560--3595 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
3550 TGAAGACTTA
3560 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
3579 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
3596 ATTATCTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:15927 original size:33 final size:33
Alignment explanation
Indices: 15885--15951 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
15875 CCAAAACTAT
15885 AAGAAAGCTGCCACTAACGACTTTTTTTTTATC
1 AAGAAAGCTGCCACTAACGACTTTTTTTTTATC
15918 AAGAAAGCTGCCACTAACGACTTTTTTTTTATC
1 AAGAAAGCTGCCACTAACGACTTTTTTTTTATC
15951 A
1 A
15952 GGAGGGTTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (33 bp):
AAGAAAGCTGCCACTAACGACTTTTTTTTTATC
Found at i:25004 original size:24 final size:24
Alignment explanation
Indices: 24973--25023 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
24963 CAACCAAATA
* *
24973 AAATCGAATTGTTTTTTTTTCCTT
1 AAATCGAATTGGTTTTTTTCCCTT
24997 AAATCGAATTGGTTTTTTTCCCTT
1 AAATCGAATTGGTTTTTTTCCCTT
25021 AAA
1 AAA
25024 AAGTATTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.25, C:0.14, G:0.10, T:0.51
Consensus pattern (24 bp):
AAATCGAATTGGTTTTTTTCCCTT
Found at i:25031 original size:24 final size:24
Alignment explanation
Indices: 24978--25031 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
24968 AAATAAAATC
* * **
24978 GAATTGTTTTTTTTTCCTTAAATC
1 GAATTGGTTTTTTTCCCTTAAAAA
25002 GAATTGGTTTTTTTCCCTTAAAAA
1 GAATTGGTTTTTTTCCCTTAAAAA
*
25026 GTATTG
1 GAATTG
25032 ATTGATTACA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.11, G:0.13, T:0.52
Consensus pattern (24 bp):
GAATTGGTTTTTTTCCCTTAAAAA
Found at i:28725 original size:21 final size:22
Alignment explanation
Indices: 28683--28726 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 22
28673 CTGAATTAAA
28683 ATTCTTACATAATACCACCAACCC
1 ATTCTTACATAAT--CACCAACCC
28707 ATTCTTACATAAT-ACCAACC
1 ATTCTTACATAATCACCAACC
28727 AAACTAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 7 0.35
24 13 0.65
ACGTcount: A:0.39, C:0.34, G:0.00, T:0.27
Consensus pattern (22 bp):
ATTCTTACATAATCACCAACCC
Found at i:30748 original size:72 final size:72
Alignment explanation
Indices: 30670--30821 Score: 204
Period size: 72 Copynumber: 2.1 Consensus size: 72
30660 GTTTTTGCAA
30670 ACAAACCATC-AAGATCAATTTTTGACAATCT-AAAAATTTCAGCAGAAAA-TTTCGCATCCAAA
1 ACAAACCATCAAAG-TCAATTTTTGACAATCTCAAAAATTT-AGCAGAAAACTTT-GCAT-CAAA
30732 -CTAGAATCCC
62 CCTAGAATCCC
* * *
30742 ACAAACCTTCAAAGTCAATTTTTGACAATCTCAAGACTTTAGCAGAAAACTTTGCATCAAACCTA
1 ACAAACCATCAAAGTCAATTTTTGACAATCTCAAAAATTTAGCAGAAAACTTTGCATCAAACCTA
*
30807 GAATCCG
66 GAATCCC
30814 ACAAACCA
1 ACAAACCA
30822 AGATCTTCAA
Statistics
Matches: 71, Mismatches: 5, Indels: 8
0.85 0.06 0.10
Matches are distributed among these distances:
71 4 0.06
72 55 0.77
73 12 0.17
ACGTcount: A:0.42, C:0.24, G:0.09, T:0.24
Consensus pattern (72 bp):
ACAAACCATCAAAGTCAATTTTTGACAATCTCAAAAATTTAGCAGAAAACTTTGCATCAAACCTA
GAATCCC
Found at i:32926 original size:20 final size:20
Alignment explanation
Indices: 32901--32948 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
32891 ACATTCTTGA
32901 CCATCTTGGCGCAATCTCCT
1 CCATCTTGGCGCAATCTCCT
32921 CCATCTTGGCGCAATCTCCT
1 CCATCTTGGCGCAATCTCCT
32941 CCATCTTG
1 CCATCTTG
32949 ACCCGGGCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.15, C:0.40, G:0.15, T:0.31
Consensus pattern (20 bp):
CCATCTTGGCGCAATCTCCT
Found at i:34446 original size:17 final size:18
Alignment explanation
Indices: 34424--34457 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
34414 CGACTGCGAT
34424 AAACGC-AACACGACCGA
1 AAACGCGAACACGACCGA
*
34441 AAACGCGACCACGACCG
1 AAACGCGAACACGACCG
34458 CAATTTGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.41, C:0.38, G:0.21, T:0.00
Consensus pattern (18 bp):
AAACGCGAACACGACCGA
Found at i:42352 original size:27 final size:25
Alignment explanation
Indices: 42285--42365 Score: 98
Period size: 27 Copynumber: 3.3 Consensus size: 25
42275 ATGGGTAGAC
42285 TAATAATTATGT-TTAATTAATACTG
1 TAATAATTAT-TATTAATTAATACTG
*
42310 TAATAA-TA--ATAAATTAATACTG
1 TAATAATTATTATTAATTAATACTG
42332 TAATAATTAGTTTATTAATTAATACTG
1 TAATAATTA--TTATTAATTAATACTG
42359 TAATAAT
1 TAATAAT
42366 AAACTCACAC
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
22 18 0.38
23 2 0.04
24 2 0.04
25 6 0.12
27 20 0.42
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (25 bp):
TAATAATTATTATTAATTAATACTG
Found at i:42365 original size:15 final size:15
Alignment explanation
Indices: 42316--42365 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
42306 ACTGTAATAA
42316 TAATAAATTAATACTG
1 TAAT-AATTAATACTG
*
42332 TAATAATTAGT--T-
1 TAATAATTAATACTG
*
42344 TATTAATTAATACTG
1 TAATAATTAATACTG
42359 TAATAAT
1 TAATAAT
42366 AAACTCACAC
Statistics
Matches: 27, Mismatches: 4, Indels: 7
0.71 0.11 0.18
Matches are distributed among these distances:
12 9 0.33
13 1 0.04
14 1 0.04
15 12 0.44
16 4 0.15
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (15 bp):
TAATAATTAATACTG
Found at i:45514 original size:17 final size:17
Alignment explanation
Indices: 45492--45525 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
45482 GACGATGACC
45492 ACATTATCTATCAGGTA
1 ACATTATCTATCAGGTA
*
45509 ACATTATCTATGAGGTA
1 ACATTATCTATCAGGTA
45526 TGAGATAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (17 bp):
ACATTATCTATCAGGTA
Found at i:47357 original size:10 final size:10
Alignment explanation
Indices: 47342--47366 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
47332 TATGAGATCT
47342 GAGAAAAAGA
1 GAGAAAAAGA
47352 GAGAAAAAGA
1 GAGAAAAAGA
47362 GAGAA
1 GAGAA
47367 GGAGAAGACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (10 bp):
GAGAAAAAGA
Found at i:47500 original size:2 final size:2
Alignment explanation
Indices: 47495--47552 Score: 51
Period size: 2 Copynumber: 32.5 Consensus size: 2
47485 ATATAAACGG
47495 AT AT AT CAT AT AT AT AT AT A- AT AT AT AT -T A- AT A- AT AT A-
1 AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47533 AT A- AT AT -T AT -T AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
47553 AAGGGTCGGT
Statistics
Matches: 47, Mismatches: 0, Indels: 18
0.72 0.00 0.28
Matches are distributed among these distances:
1 8 0.17
2 37 0.79
3 2 0.04
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:47511 original size:11 final size:11
Alignment explanation
Indices: 47495--47552 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
47485 ATATAAACGG
*
47495 ATATATCATAT
1 ATATATTATAT
47506 ATATA-TATAAT
1 ATATATTAT-AT
47517 ATATATTA-AT
1 ATATATTATAT
*
47527 A-ATATAATA-
1 ATATATTATAT
47536 ATATTATTATAT
1 ATA-TATTATAT
47548 ATATA
1 ATATA
47553 AAGGGTCGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
9 6 0.16
10 7 0.18
11 20 0.53
12 5 0.13
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (11 bp):
ATATATTATAT
Found at i:47513 original size:13 final size:13
Alignment explanation
Indices: 47495--47553 Score: 61
Period size: 13 Copynumber: 4.6 Consensus size: 13
47485 ATATAAACGG
*
47495 ATATATCATATAT
1 ATATATAATATAT
47508 ATATATAATATAT
1 ATATATAATATAT
47521 AT-TAATAATATA-
1 ATAT-ATAATATAT
*
47533 ATA-ATATTATTAT
1 ATATATAATA-TAT
47546 ATATATAA
1 ATATATAA
47554 AGGGTCGGTC
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
11 5 0.13
12 5 0.13
13 25 0.66
14 3 0.08
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATAATATAT
Found at i:49947 original size:2 final size:2
Alignment explanation
Indices: 49942--49973 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
49932 ACACACACAC
49942 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
49974 TCTTAATGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51191 original size:26 final size:27
Alignment explanation
Indices: 51161--51213 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 27
51151 ATTTAGTTAT
51161 CATTTTCATTAGATTTTCA-AAGAAAA
1 CATTTTCATTAGATTTTCATAAGAAAA
*
51187 CATTTTCATTAGGTTTTCATAAGAAAA
1 CATTTTCATTAGATTTTCATAAGAAAA
51214 AAAAACAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 18 0.72
27 7 0.28
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (27 bp):
CATTTTCATTAGATTTTCATAAGAAAA
Found at i:52466 original size:11 final size:10
Alignment explanation
Indices: 52442--52480 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
52432 ATCTGTTAGC
*
52442 GAAAAAGAAA
1 GAAAAAAAAA
52452 GAAAAAAAAA
1 GAAAAAAAAA
52462 GGAAAAAAAACA
1 -GAAAAAAAA-A
52474 GAAAAAA
1 GAAAAAA
52481 GTCATACTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 9 0.35
11 16 0.62
12 1 0.04
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:56371 original size:13 final size:13
Alignment explanation
Indices: 56353--56379 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
56343 AAGACTGTTA
56353 TTCTCCCTCGAGC
1 TTCTCCCTCGAGC
56366 TTCTCCCTCGAGC
1 TTCTCCCTCGAGC
56379 T
1 T
56380 CAATATGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.44, G:0.15, T:0.33
Consensus pattern (13 bp):
TTCTCCCTCGAGC
Found at i:62958 original size:52 final size:52
Alignment explanation
Indices: 62894--62997 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
62884 ATATGTCATT
62894 AATTCATTACTATATATTCATATATAATGTACATAGACAGTATCTTATGTTA
1 AATTCATTACTATATATTCATATATAATGTACATAGACAGTATCTTATGTTA
62946 AATTCATTACTATATATTCATATATAATGTACATAGACAGTATCTTATGTTA
1 AATTCATTACTATATATTCATATATAATGTACATAGACAGTATCTTATGTTA
62998 CCATGTATGT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (52 bp):
AATTCATTACTATATATTCATATATAATGTACATAGACAGTATCTTATGTTA
Found at i:63262 original size:35 final size:35
Alignment explanation
Indices: 63223--63293 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
63213 ATAGTATGAT
63223 GTAATCATTATAATATATACTAGTGTCCGGCCCGC
1 GTAATCATTATAATATATACTAGTGTCCGGCCCGC
63258 GTAATCATTATAATATATACTAGTGTCCGGCCCGC
1 GTAATCATTATAATATATACTAGTGTCCGGCCCGC
63293 G
1 G
63294 CTTCGCTGCG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (35 bp):
GTAATCATTATAATATATACTAGTGTCCGGCCCGC
Found at i:64950 original size:49 final size:49
Alignment explanation
Indices: 64873--64970 Score: 151
Period size: 49 Copynumber: 2.0 Consensus size: 49
64863 TAAATATTAT
* * *
64873 TCAGTAGCTCTACCTGGATGGTTAAAAGTTTAAGTGAAACCTCATCATC
1 TCAGCAGCTCTACCTGAATGATTAAAAGTTTAAGTGAAACCTCATCATC
* *
64922 TCAGCAGCTCTACCTGAATTATTAAAAGTTTAAGTGAAAGCTCATCATC
1 TCAGCAGCTCTACCTGAATGATTAAAAGTTTAAGTGAAACCTCATCATC
64971 ATCTGTTTCC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (49 bp):
TCAGCAGCTCTACCTGAATGATTAAAAGTTTAAGTGAAACCTCATCATC
Found at i:70350 original size:21 final size:21
Alignment explanation
Indices: 70326--70366 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
70316 TGGAGTTGTG
70326 AGATTAAACACTGTACAGATC
1 AGATTAAACACTGTACAGATC
***
70347 AGATTAGGTACTGTACAGAT
1 AGATTAAACACTGTACAGAT
70367 GAGCAATAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.27
Consensus pattern (21 bp):
AGATTAAACACTGTACAGATC
Found at i:70676 original size:18 final size:18
Alignment explanation
Indices: 70642--70676 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
70632 TACTAATTAA
*
70642 AAAACAAAAGTAAAAAAG
1 AAAACAAAAGAAAAAAAG
*
70660 AAAAGAAAAGAAAAAAA
1 AAAACAAAAGAAAAAAA
70677 ATAAAATAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.83, C:0.03, G:0.11, T:0.03
Consensus pattern (18 bp):
AAAACAAAAGAAAAAAAG
Found at i:71743 original size:27 final size:27
Alignment explanation
Indices: 71712--71801 Score: 110
Period size: 27 Copynumber: 3.2 Consensus size: 27
71702 ATTTATAATG
71712 ATATAACATTCTCAGGTATATATATAT
1 ATATAACATTCTCAGGTATATATATAT
* *
71739 ATAT-ATATTGATCAGGTATATATTTATAAT
1 ATATAACATT-CTCAGGTATATA--TAT-AT
71769 GATATAACATTCTCAGGTATATATATAT
1 -ATATAACATTCTCAGGTATATATATAT
71797 ATATA
1 ATATA
71802 TATATATATA
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
26 4 0.08
27 20 0.38
28 2 0.04
29 6 0.11
30 2 0.04
31 15 0.28
32 4 0.08
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.42
Consensus pattern (27 bp):
ATATAACATTCTCAGGTATATATATAT
Found at i:71785 original size:31 final size:30
Alignment explanation
Indices: 71700--71805 Score: 121
Period size: 31 Copynumber: 3.5 Consensus size: 30
71690 TCTTAATGAG
71700 ATATTTATAATGATATAACATTCTCAGGTAT
1 ATATTTATAAT-ATATAACATTCTCAGGTAT
* *
71731 ATA--TAT-ATATAT-ATATTGATCAGGTAT
1 ATATTTATAATATATAACATT-CTCAGGTAT
71758 ATATTTATAATGATATAACATTCTCAGGTAT
1 ATATTTATAAT-ATATAACATTCTCAGGTAT
*
71789 ATATATATATATATATA
1 ATATTTATA-ATATATA
71806 TATATATACT
Statistics
Matches: 63, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
26 4 0.06
27 15 0.24
28 2 0.03
29 6 0.10
30 2 0.03
31 28 0.44
32 6 0.10
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.43
Consensus pattern (30 bp):
ATATTTATAATATATAACATTCTCAGGTAT
Found at i:71793 original size:2 final size:2
Alignment explanation
Indices: 71786--71821 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
71776 CATTCTCAGG
71786 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA T
71822 TATTTTTAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:77055 original size:17 final size:18
Alignment explanation
Indices: 77025--77066 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
77015 CTCTCTCTCT
77025 CTCTCTCGCTTCCCTTGCA
1 CTCTCTCGCTTCCC-TGCA
*
77044 CTCTCT-GC-TCCCTGCG
1 CTCTCTCGCTTCCCTGCA
77060 CTCTCTC
1 CTCTCTC
77067 TTTTCTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 9 0.43
17 4 0.19
18 2 0.10
19 6 0.29
ACGTcount: A:0.02, C:0.50, G:0.12, T:0.36
Consensus pattern (18 bp):
CTCTCTCGCTTCCCTGCA
Found at i:77276 original size:12 final size:12
Alignment explanation
Indices: 77244--77277 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
77234 TAAAGGGTTG
77244 ATATATATTTTT
1 ATATATATTTTT
*
77256 TTATGATATTTTT
1 ATAT-ATATTTTT
77269 ATATATATT
1 ATATATATT
77278 GCATGACCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (12 bp):
ATATATATTTTT
Found at i:77334 original size:25 final size:27
Alignment explanation
Indices: 77298--77353 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
77288 TTGTATAATT
77298 TATTTTTCA-TTTGAATATTTTATCTA
1 TATTTTTCATTTTGAATATTTTATCTA
*
77324 TATTTTT-ATTTTTTAATATTTTATCTA
1 TATTTTTCA-TTTTGAATATTTTATCTA
77351 TAT
1 TAT
77354 CTATATCTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 1 0.04
26 7 0.26
27 19 0.70
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (27 bp):
TATTTTTCATTTTGAATATTTTATCTA
Found at i:82869 original size:4 final size:4
Alignment explanation
Indices: 82860--82898 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
82850 CTTTTCTTTT
82860 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATT
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATT
82899 TTTTTCAAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (4 bp):
ATTA
Found at i:83710 original size:7 final size:7
Alignment explanation
Indices: 83698--83729 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
83688 TAATGAAATT
83698 AAAAGGG
1 AAAAGGG
83705 AAAAGGG
1 AAAAGGG
83712 AAAAGGG
1 AAAAGGG
83719 AAAAGGG
1 AAAAGGG
83726 AAAA
1 AAAA
83730 ACTCAATTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (7 bp):
AAAAGGG
Found at i:85152 original size:21 final size:21
Alignment explanation
Indices: 85109--85155 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
85099 AAGGATCGAG
*
85109 CTGGGCGCTGAGCCTTGTCGC
1 CTGGGCGCTGAGCATTGTCGC
*
85130 CTGGGCGCTGAGGCATT-TTGC
1 CTGGGCGCTGA-GCATTGTCGC
85151 CTGGG
1 CTGGG
85156 TGCCCAGCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.06, C:0.28, G:0.40, T:0.26
Consensus pattern (21 bp):
CTGGGCGCTGAGCATTGTCGC
Done.