Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1519
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: 26728
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Found at i:6373 original size:79 final size:79
Alignment explanation
Indices: 6172--6400 Score: 205
Period size: 79 Copynumber: 2.9 Consensus size: 79
6162 TGGGGATAAC
* * * *
6172 AACAGGG-CTGGAGTATCCCCGATTATGAAAAATTGGTGTTTT-GAAAATAAAATCGAGGTTGGA
1 AACAGGGTC-GGAGTATCCCCGATTGTGAAAAAATGGTGTTTTAG-AAATAAAACCGAGGTTAGA
*
6235 GTATCCCCTCAAAAAT
64 GTATCCCCGCAAAAAT
* * * ** * * **
6251 AACGGGGTTGGAGTATCCTCGATTGTG-GTAAATCGATGCTTTAGAAATAAGGCCG-GAGTTAGA
1 AACAGGGTCGGAGTATCCCCGATTGTGAAAAAAT-GGTGTTTTAGAAATAAAACCGAG-GTTAGA
* *
6314 GTATCCTCGCGAAAAT
64 GTATCCCCGCAAAAAT
* ** * *
6330 AACAGGGTCGGAGTGTCCCCGATTGTGAAAAAATGGTGTTTTAGAAATAAAATTGGGGTTGGAGT
1 AACAGGGTCGGAGTATCCCCGATTGTGAAAAAATGGTGTTTTAGAAATAAAACCGAGGTTAGAGT
6395 ATCCCC
66 ATCCCC
6401 AATTATGAGA
Statistics
Matches: 114, Mismatches: 30, Indels: 12
0.73 0.19 0.08
Matches are distributed among these distances:
78 4 0.04
79 104 0.91
80 6 0.05
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (79 bp):
AACAGGGTCGGAGTATCCCCGATTGTGAAAAAATGGTGTTTTAGAAATAAAACCGAGGTTAGAGT
ATCCCCGCAAAAAT
Found at i:6424 original size:130 final size:130
Alignment explanation
Indices: 6253--6530 Score: 337
Period size: 130 Copynumber: 2.1 Consensus size: 130
6243 TCAAAAATAA
* * * * * * *
6253 CGGGGTTGGAGTATCCTCGATTGTGGTAAATCGATGCTTTAGAAATAAGGCC-GGAGTTAGAGTA
1 CGGGGTTGGAGTATCCCCAATTATGGTAAATCAATACTTTAGAAATAAAGCCAGG-GTTAAAGTA
* * *
6317 TCCTCGCGAAAATAACAGGG-TCGGAGTGTCCCCGATTGTGAAAAAATGGTGTTTTAGAAATAAA
65 TCCTCGCGAAAATAA-AGGGATCGGAGTATCCCCGATTATGAAAAAATGATGTTTTAGAAATAAA
*
6381 AT
129 AC
* *
6383 TGGGGTTGGAGTATCCCCAATTATGAG-AAATCAATATTTTAGAAATAAAGCCAGGGTTAAAGTA
1 CGGGGTTGGAGTATCCCCAATTATG-GTAAATCAATACTTTAGAAATAAAGCCAGGGTTAAAGTA
* * * * *
6447 TCCTCTCGAAAATAAAGGGATTGGAGTATCCTCGATTATGAAAAATTGATGTTTTGGAAATAAAA
65 TCCTCGCGAAAATAAAGGGATCGGAGTATCCCCGATTATGAAAAAATGATGTTTTAGAAATAAAA
6512 C
130 C
*
6513 CGAGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
6531 GTGATGAAAA
Statistics
Matches: 125, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
129 4 0.03
130 118 0.94
131 3 0.02
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.28
Consensus pattern (130 bp):
CGGGGTTGGAGTATCCCCAATTATGGTAAATCAATACTTTAGAAATAAAGCCAGGGTTAAAGTAT
CCTCGCGAAAATAAAGGGATCGGAGTATCCCCGATTATGAAAAAATGATGTTTTAGAAATAAAAC
Found at i:12880 original size:27 final size:27
Alignment explanation
Indices: 12848--12903 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
12838 ACAAGGAAAT
12848 GTCTTCTGTCTCTTGGCAGCCAAATTA
1 GTCTTCTGTCTCTTGGCAGCCAAATTA
12875 GTCTTCTGTCTCTTGGCAGCCAAATTA
1 GTCTTCTGTCTCTTGGCAGCCAAATTA
12902 GT
1 GT
12904 AGCCCCAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.38
Consensus pattern (27 bp):
GTCTTCTGTCTCTTGGCAGCCAAATTA
Found at i:14562 original size:15 final size:17
Alignment explanation
Indices: 14542--14580 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
14532 AAGTAAACAC
14542 AAAAAACAA-A-ACAAA
1 AAAAAACAACACACAAA
14557 AAAAAACAACACACAAA
1 AAAAAACAACACACAAA
14574 AGAAAAA
1 A-AAAAA
14581 GTGCAAAGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 1 0.05
17 6 0.29
18 5 0.24
ACGTcount: A:0.82, C:0.15, G:0.03, T:0.00
Consensus pattern (17 bp):
AAAAAACAACACACAAA
Found at i:15942 original size:31 final size:31
Alignment explanation
Indices: 15872--16179 Score: 340
Period size: 31 Copynumber: 9.9 Consensus size: 31
15862 ATACCTTCTT
* * *
15872 AAAGTCCACCACTCAGTGTCATTTTGTC-CC
1 AAAGTCCACGACTCAGTGGCATTTTTTCTCC
*
15902 AAAGCCCACGACTCAGTGGCATTTTTTCTCC
1 AAAGTCCACGACTCAGTGGCATTTTTTCTCC
*
15933 AAAGTCCACGACTCAGTGGCATTTTTTTGTCC
1 AAAGTCCACGACTCAGTGGCA-TTTTTTCTCC
*
15965 AAAGTCCATGACTCAGTGGCATTTTTTCTCC
1 AAAGTCCACGACTCAGTGGCATTTTTTCTCC
* *
15996 AAAGTCCACAACTCAGTGGCAATCTATTT-T-C
1 AAAGTCCACGACTCAGTGGC-AT-TTTTTCTCC
*
16027 AAAGTCCACGACTCAGTGGCATTTTGTC-CC
1 AAAGTCCACGACTCAGTGGCATTTTTTCTCC
* *
16057 AAAGCCCATGACTCAGTGGCATTTTTTCTCC
1 AAAGTCCACGACTCAGTGGCATTTTTTCTCC
* * *
16088 AAAGTCCACAACTTAGTGGCAATCTCTTT-T-C
1 AAAGTCCACGACTCAGTGGC-AT-TTTTTCTCC
* *
16119 AAAGTCCACGACTCAGTGGCATCTTTTCTTC
1 AAAGTCCACGACTCAGTGGCATTTTTTCTCC
* * * *
16150 AAAGCCCACAACTCTGTGGCACCTTTTTCT
1 AAAGTCCACGACTCAGTGGCA-TTTTTTCT
16180 TTTCAAAGCC
Statistics
Matches: 235, Mismatches: 31, Indels: 22
0.82 0.11 0.08
Matches are distributed among these distances:
29 6 0.03
30 55 0.23
31 125 0.53
32 41 0.17
33 8 0.03
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31
Consensus pattern (31 bp):
AAAGTCCACGACTCAGTGGCATTTTTTCTCC
Found at i:16093 original size:92 final size:91
Alignment explanation
Indices: 15882--16232 Score: 383
Period size: 92 Copynumber: 3.8 Consensus size: 91
15872 AAAGTCCACC
* * * *
15882 ACTCAGTGTCATTTTGTC-CCAAAGCCCACGACTCAGTGGCAT-TTTTTCTCCAAAGTCCACGAC
1 ACTCAGTGGCATTTTTTCTCCAAAGCCCACAACTCAGTGGCATCTCTTT-T-CAAAGTCCACGAC
*
15945 TCAGTGGCATTTTTTTGT-CCAAAGTCCATG
64 TCAGTGGCA---TTTTGTCCCAAAGCCCATG
* *
15975 ACTCAGTGGCATTTTTTCTCCAAAGTCCACAACTCAGTGGCAATCTATTTTCAAAGTCCACGACT
1 ACTCAGTGGCATTTTTTCTCCAAAGCCCACAACTCAGTGGC-ATCTCTTTTCAAAGTCCACGACT
16040 CAGTGGCATTTTGTCCCAAAGCCCATG
65 CAGTGGCATTTTGTCCCAAAGCCCATG
* *
16067 ACTCAGTGGCATTTTTTCTCCAAAGTCCACAACTTAGTGGCAATCTCTTTTCAAAGTCCACGACT
1 ACTCAGTGGCATTTTTTCTCCAAAGCCCACAACTCAGTGGC-ATCTCTTTTCAAAGTCCACGACT
* **
16132 CAGTGGCATCTTT-TCTTCAAAGCCCACA
65 CAGTGGCAT-TTTGTC-CCAAAGCCCATG
* * * * *
16160 ACTCTGTGGCACCTTTTTCTTTTCAAAGCCCACAACTCCGTGGCATC-CTTTT--AAGTCCACAA
1 ACTCAGTGGCA--TTTTT-TCTCCAAAGCCCACAACTCAGTGGCATCTCTTTTCAAAGTCCACGA
*
16222 CTCTGTGGCAT
63 CTCAGTGGCAT
16233 CTTTTTCCTT
Statistics
Matches: 230, Mismatches: 19, Indels: 19
0.86 0.07 0.07
Matches are distributed among these distances:
91 6 0.03
92 104 0.45
93 38 0.17
94 47 0.20
95 11 0.05
96 24 0.10
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31
Consensus pattern (91 bp):
ACTCAGTGGCATTTTTTCTCCAAAGCCCACAACTCAGTGGCATCTCTTTTCAAAGTCCACGACTC
AGTGGCATTTTGTCCCAAAGCCCATG
Found at i:16190 original size:34 final size:34
Alignment explanation
Indices: 16112--16598 Score: 462
Period size: 34 Copynumber: 14.9 Consensus size: 34
16102 AGTGGCAATC
* * * *
16112 TCTTTTCAAAGTCCACGACTCAGTGGCATC-TTT
1 TCTTTTCAAAGCCCACAACTCCGTGGCACCTTTT
*
16145 TC--TTCAAAGCCCACAACTCTGTGGCACCTTTT
1 TCTTTTCAAAGCCCACAACTCCGTGGCACCTTTT
16177 TCTTTTCAAAGCCCACAACTCCGTGGCA-----T
1 TCTTTTCAAAGCCCACAACTCCGTGGCACCTTTT
* * * *
16206 CCTTTT--AAGTCCACAACTCTGTGGCATCTTTT
1 TCTTTTCAAAGCCCACAACTCCGTGGCACCTTTT
* ** * *
16238 TC-CTTCTTAGCCCACAACTCTGTGGCTCTCTTTT
1 TCTTTTCAAAGCCCACAACTCCGTGGCAC-CTTTT
*
16272 TCTTTTC-AAGTCCACAACTCCGTGGCACCTTTT
1 TCTTTTCAAAGCCCACAACTCCGTGGCACCTTTT
* *
16305 TCTTTTTAAAGCCCACAACTCTGTGGCACCTTTT
1 TCTTTTCAAAGCCCACAACTCCGTGGCACCTTTT
16339 TCTTTTCAAAGCCCACAACTCCGTGGCA-----T
1 TCTTTTCAAAGCCCACAACTCCGTGGCACCTTTT
* * * *
16368 CCTTTT--AAGTCCACAACTCTGTGGCATCTTTT
1 TCTTTTCAAAGCCCACAACTCCGTGGCACCTTTT
* ** * *
16400 TC-CTTCTTAGCCCACAACTCTGTGGCTCTCTTTT
1 TCTTTTCAAAGCCCACAACTCCGTGGCAC-CTTTT
*
16434 TCTTTTC-AAGTCCACAACTCCGTGGCACCTTTT
1 TCTTTTCAAAGCCCACAACTCCGTGGCACCTTTT
*
16467 TCTTTTTAAAGCCCACAACTCCGTGGCACCTTTT
1 TCTTTTCAAAGCCCACAACTCCGTGGCACCTTTT
* *
16501 TCTTTTTAAAGCCCACAACTCCGTGGCACTTTTTT
1 TCTTTTCAAAGCCCACAACTCCGTGGCAC-CTTTT
* *
16536 TCTTTTCAAAGTCCACAACTCTGTGGCATCCTTTT
1 TCTTTTCAAAGCCCACAACTCCGTGGCA-CCTTTT
* * *
16571 CCTTTT--AAGTCCACAACCCCGTGGCACC
1 TCTTTTCAAAGCCCACAACTCCGTGGCACC
16599 CCCTTCTAAA
Statistics
Matches: 381, Mismatches: 48, Indels: 51
0.79 0.10 0.11
Matches are distributed among these distances:
27 36 0.09
29 12 0.03
31 26 0.07
32 11 0.03
33 76 0.20
34 175 0.46
35 44 0.12
36 1 0.00
ACGTcount: A:0.19, C:0.32, G:0.13, T:0.36
Consensus pattern (34 bp):
TCTTTTCAAAGCCCACAACTCCGTGGCACCTTTT
Found at i:16306 original size:128 final size:127
Alignment explanation
Indices: 16155--16615 Score: 440
Period size: 128 Copynumber: 3.5 Consensus size: 127
16145 TCTTCAAAGC
*
16155 CCACAACTCTGTGGCACCTTTTTCTTTTCAAAGCCCACAACTCCGTGGCA-TCCTTTT-AAGTCC
1 CCACAACTCTGTGGCACCTTTTTCTTTTC-AAGCCCACAACTCCGTGGCATTCCTTTTAAAGCCC
*
16218 ACAACTCTGTGGCATCTTTTTCCTTCTT-AGCCCACAACTCTGTGGCTCTCTTTTTCTTTTCAAG
65 ACAACTCCGTGGCA-CTTTTTCCTT-TTAAGCCCACAACTCTGTGGCTCT-TTTTTCTTTTCAAG
16282 T
127 T
* * * *
16283 CCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCTGTGGCACCTTTTTCTTTTCAA
1 CCACAACTCTGTGGCACCTTTTTC-TTTTCAAGCCCACAACTCCGTGGCA----TTCCTTTT-AA
* *
16348 AGCCCACAACTCCGTGGCA-----TCCTTTTAAGTCCACAACTCTGTGGCATCTTTTTCCTTCTT
60 AGCCCACAACTCCGTGGCACTTTTTCCTTTTAAGCCCACAACTCTGTGGC-TCTTTTTTCTT-TT
*
16408 --AGC
123 CAAGT
* * *
16411 CCACAACTCTGTGGCTCTCTTTTTCTTTTCAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAA
1 CCACAACTCTGTGGCAC-CTTTTTCTTTTCAAGCCCACAACTCCGTGGCA-----TTCCTTTTAA
* * *
16476 AGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTTTTTTTCTTT
60 AGCCCACAACTCCGTGGCA-CTTTTTCCTTTT-AAGCCCACAACTCTGTGGCTC-TTTTTTCTTT
16541 TCAAAGT
122 TC-AAGT
* * * ** *
16548 CCACAACTCTGTGGCATCCTTTTCCTTTT-AAGTCCACAACCCCGTGGCACCCCCTTCTAAAGCC
1 CCACAACTCTGTGGCA-CCTTTTTCTTTTCAAGCCCACAACTCCGTGGCA-TTCCTTTTAAAGCC
16612 CACA
64 CACA
16616 CAAGTCGGTG
Statistics
Matches: 277, Mismatches: 31, Indels: 46
0.78 0.09 0.13
Matches are distributed among these distances:
128 104 0.38
129 49 0.18
130 5 0.02
132 14 0.05
133 6 0.02
134 9 0.03
135 43 0.16
136 19 0.07
137 27 0.10
138 1 0.00
ACGTcount: A:0.19, C:0.33, G:0.12, T:0.35
Consensus pattern (127 bp):
CCACAACTCTGTGGCACCTTTTTCTTTTCAAGCCCACAACTCCGTGGCATTCCTTTTAAAGCCCA
CAACTCCGTGGCACTTTTTCCTTTTAAGCCCACAACTCTGTGGCTCTTTTTTCTTTTCAAGT
Found at i:16330 original size:162 final size:162
Alignment explanation
Indices: 16112--16587 Score: 753
Period size: 162 Copynumber: 2.9 Consensus size: 162
16102 AGTGGCAATC
* * * *
16112 TCTTTTCAAAGTCCACGACTCAGTGGCATC-TTTTC--TTCAAAGCCCACAACTCTGTGGCACCT
1 TCTTTTC-AAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCTGTGGCACCT
16174 TTTTCTTTTCAAAGCCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCTGTGGCATCTTTTT
65 TTTTCTTTTCAAAGCCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCTGTGGCATCTTTTT
16239 CCTTCTTAGCCCACAACTCTGTGGCTCTCTTTT
130 CCTTCTTAGCCCACAACTCTGTGGCTCTCTTTT
16272 TCTTTTCAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCTGTGGCACCTT
1 TCTTTTCAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCTGTGGCACCTT
16337 TTTCTTTTCAAAGCCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCTGTGGCATCTTTTTC
66 TTTCTTTTCAAAGCCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCTGTGGCATCTTTTTC
16402 CTTCTTAGCCCACAACTCTGTGGCTCTCTTTT
131 CTTCTTAGCCCACAACTCTGTGGCTCTCTTTT
*
16434 TCTTTTCAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACCTT
1 TCTTTTCAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCTGTGGCACCTT
* *
16499 TTTCTTTTTAAAGCCCACAACTCCGTGGCACTTTTTTTCTTTTCAAAGTCCACAACTCTGTGGCA
66 TTTCTTTTCAAAGCCCACAACTCCGTGGCA------TCCTTTT--AAGTCCACAACTCTGTGGCA
* *
16564 TCCTTTTCCTT-TTAAGTCCACAAC
123 TCTTTTTCCTTCTT-AGCCCACAAC
16588 CCCGTGGCAC
Statistics
Matches: 295, Mismatches: 9, Indels: 14
0.93 0.03 0.04
Matches are distributed among these distances:
159 19 0.06
160 12 0.04
162 217 0.74
168 6 0.02
169 2 0.01
170 39 0.13
ACGTcount: A:0.20, C:0.32, G:0.12, T:0.37
Consensus pattern (162 bp):
TCTTTTCAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCTGTGGCACCTT
TTTCTTTTCAAAGCCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCTGTGGCATCTTTTTC
CTTCTTAGCCCACAACTCTGTGGCTCTCTTTT
Found at i:16645 original size:33 final size:33
Alignment explanation
Indices: 16603--16669 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
16593 GGCACCCCCT
16603 TCTAAAGCCCACACAAGTCGGTGGCAACCATTC
1 TCTAAAGCCCACACAAGTCGGTGGCAACCATTC
*
16636 TCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
1 TCTAAAGCCCACACAAGTCGGTGGCAACCATTC
16669 T
1 T
16670 AAGCCCAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.28, C:0.34, G:0.18, T:0.19
Consensus pattern (33 bp):
TCTAAAGCCCACACAAGTCGGTGGCAACCATTC
Found at i:16776 original size:43 final size:43
Alignment explanation
Indices: 16664--17362 Score: 642
Period size: 43 Copynumber: 15.1 Consensus size: 43
16654 CGGTGGCAAC
* *
16664 CCTTCTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTA
1 CCTT-TAAGTCCAATGTCGCTGGCCTTGAATCAGCATATT-G-G-C---A
* *
16714 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
1 CCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCA
*
16757 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
1 CCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCA
* * * *
16800 TCTTTTTCTTTAAGACCAATGTCGTTGGCCTTGAACCAGCACATTGGCA
1 -C-----CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCA
* * *
16849 CCTTTAAGCCCAATATTGCTGGCCTTGAATCAGCATATTGGCA
1 CCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCA
* *
16892 CCTTTGTTTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
1 CC------TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCA
* *
16941 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCA
1 CCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCA
16984 CCTTTGTCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCA
1 -C-----CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCA
* *
17033 CCTCATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
1 ---C--CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCA
* *
17081 CCTTTAAGTCCAATATCGCTGGTCTTGAATCAGCATATTGGCA
1 CCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCA
17124 CCTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCA
1 ---C--CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCA
* *
17172 CCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCGCCTTCGTCA
1 CCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATT---G-----G-CA
* ** ** * * *
17224 TCTTTAAAACCCAATGTCATTGGCCTTAAATCAACACATTGGCATTA
1 CCTTT-AAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGC---A
* * *
17271 TGCTTTAAGTCCAATGTCGCTAGCCTTGAATCAGCACATTGGCA
1 -CCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCA
* *
17315 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCG
1 CCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCA
17358 CCTTT
1 CCTTT
17363 GTCATCTTTT
Statistics
Matches: 549, Mismatches: 61, Indels: 85
0.79 0.09 0.12
Matches are distributed among these distances:
43 233 0.42
44 4 0.01
45 3 0.01
46 3 0.01
47 32 0.06
48 87 0.16
49 148 0.27
50 4 0.01
51 2 0.00
52 6 0.01
53 27 0.05
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.31
Consensus pattern (43 bp):
CCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCA
Found at i:16831 original size:92 final size:92
Alignment explanation
Indices: 16664--17414 Score: 812
Period size: 92 Copynumber: 8.0 Consensus size: 92
16654 CGGTGGCAAC
* * *
16664 CCTTCTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTATCTTTAAGTCCAATG
1 CCTT-TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCTTTAAGTCCAATG
16729 TCGCTGGCCTTGAATCAGCACATTGGCA
65 TCGCTGGCCTTGAATCAGCACATTGGCA
* *
16757 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTTTTCTTTAAGACCAATGT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCTTTAAGTCCAATGT
* *
16822 CGTTGGCCTTGAACCAGCACATTGGCA
66 CGCTGGCCTTGAATCAGCACATTGGCA
* * *
16849 CCTTTAAGCCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTTGTT-TTTAAGACCAATG
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT-TTCTTTAAGTCCAATG
16913 TCGCTGGCCTTGAATCAGCACATTGGCA
65 TCGCTGGCCTTGAATCAGCACATTGGCA
* *
16941 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCACCTTTGTCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCTTTAAGTCCAATGT
*
17006 CGCTGGCCTTGAATCAGCATATTGGCA
66 CGCTGGCCTTGAATCAGCACATTGGCA
* * *
17033 CCTCATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-C-----CTTTAAGTCC
1 ---C--CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCTTTAAGTCC
* * *
17092 AATATCGCTGGTCTTGAATCAGCATATTGGCA
61 AATGTCGCTGGCCTTGAATCAGCACATTGGCA
*
17124 CCTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCA-C-----CTTTAAGTCC
1 ---C--CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCTTTAAGTCC
* * *
17183 AATATCGTTGGCCTTGAATCAGCATATTGGCGCCTTCGTCA
61 AATGTCGCTGGCCTTGAATCAGCACATT---G-----G-CA
* ** * ** * * * * *
17224 TCTTTAAAACCCAATGTCATTGGCCTTAAATCAACACATTGGCA--TTATGCTTTAAGTCCAATG
1 CCTTT-AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCTTTAAGTCCAATG
*
17287 TCGCTAGCCTTGAATCAGCACATTGGCA
65 TCGCTGGCCTTGAATCAGCACATTGGCA
* *
17315 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTTAAGTCTA
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT-T--TC-TTTAAGTCCA
**
17380 ATGTCATTGGCCTTGAATCAGCACATTGGCA
62 ATGTCGCTGGCCTTGAATCAGCACATTGGCA
17411 CCTT
1 CCTT
17415 CATCTTTAAC
Statistics
Matches: 574, Mismatches: 56, Indels: 53
0.84 0.08 0.08
Matches are distributed among these distances:
90 29 0.05
91 130 0.23
92 252 0.44
93 7 0.01
94 1 0.00
95 6 0.01
96 73 0.13
97 39 0.07
99 1 0.00
100 36 0.06
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (92 bp):
CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCTTTAAGTCCAATGT
CGCTGGCCTTGAATCAGCACATTGGCA
Found at i:17124 original size:91 final size:91
Alignment explanation
Indices: 16991--17362 Score: 457
Period size: 91 Copynumber: 4.0 Consensus size: 91
16981 GCACCTTTGT
*
16991 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTCATCTTTAAGACCAATGTCG
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCATCTTTAAGACCAATGTCG
17056 CTGGCCTTGAATCAGCACATTGGCAC
66 CTGGCCTTGAATCAGCACATTGGCAC
* *
17082 CTTTAAGTCCAATATCGCTGGTCTTGAATCAGCATATTGGCACCTCATCTTTAAGTCCAATGTCG
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCATCTTTAAGACCAATGTCG
*
17147 CTGGCCTTGAATCAGCATATTGGCAC
66 CTGGCCTTGAATCAGCACATTGGCAC
* * *
17173 CTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAAACCCAA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC-AC--C-TCATCTTTAAGA-CCAA
** * * *
17238 TGTCATTGGCCTTAAATCAACACATTGGCATTATG
61 TGTCGCTGGCCTTGAATCAGCACATTGGC---A-C
* * * * *
17273 CTTTAAGTCCAATGTCGCTAGCCTTGAATCAGCACATTGGCA---C--CTTTAAGTCCAATATCG
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCATCTTTAAGACCAATGTCG
* *
17333 CTGGCCTTGAATCAGCATATTGGCGC
66 CTGGCCTTGAATCAGCACATTGGCAC
17359 CTTT
1 CTTT
17363 GTCATCTTTT
Statistics
Matches: 242, Mismatches: 30, Indels: 23
0.82 0.10 0.08
Matches are distributed among these distances:
86 4 0.02
90 27 0.11
91 132 0.55
92 1 0.00
93 1 0.00
94 1 0.00
95 10 0.04
96 28 0.12
99 1 0.00
100 37 0.15
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (91 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCATCTTTAAGACCAATGTCG
CTGGCCTTGAATCAGCACATTGGCAC
Found at i:17340 original size:143 final size:143
Alignment explanation
Indices: 17130--17410 Score: 472
Period size: 143 Copynumber: 2.0 Consensus size: 143
17120 GGCACCTCAT
* * *
17130 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTTAAGTCCAATATCGTTGGC
1 CTTTAAGTCCAATGTCGCTAGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGC
17195 CTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAAACCCAATGTCATTGGCCTTAAATCAACA
66 CTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAAACCCAATGTCATTGGCCTTAAATCAACA
17260 CATTGGCATTATG
131 CATTGGCATTATG
17273 CTTTAAGTCCAATGTCGCTAGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGC
1 CTTTAAGTCCAATGTCGCTAGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGC
* * ** * * *
17338 CTTGAATCAGCATATTGGCGCCTTTGTCATCTTTTAAGTCTAATGTCATTGGCCTTGAATCAGCA
66 CTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAAACCCAATGTCATTGGCCTTAAATCAACA
17403 CATTGGCA
131 CATTGGCA
17411 CCTTCATCTT
Statistics
Matches: 128, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
143 128 1.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (143 bp):
CTTTAAGTCCAATGTCGCTAGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGC
CTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAAACCCAATGTCATTGGCCTTAAATCAACA
CATTGGCATTATG
Found at i:18253 original size:19 final size:18
Alignment explanation
Indices: 18228--18292 Score: 68
Period size: 19 Copynumber: 3.8 Consensus size: 18
18218 ATTTCAACGA
18228 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
18246 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
*
18262 --TATATCGATACATAAG
1 TTTGTATCGATACATAAG
18278 TTTTGTATCGATACA
1 -TTTGTATCGATACA
18293 ATGTATCACT
Statistics
Matches: 38, Mismatches: 2, Indels: 13
0.72 0.04 0.25
Matches are distributed among these distances:
13 10 0.26
15 2 0.05
17 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.38
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:18268 original size:32 final size:32
Alignment explanation
Indices: 18232--18299 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
18222 CAACGATTTG
18232 TATCGATACATAAGTGTTGTATCGATACAATA
1 TATCGATACATAAGTGTTGTATCGATACAATA
* *
18264 TATCGATACATAAGTTTTGTATCGATACAATG
1 TATCGATACATAAGTGTTGTATCGATACAATA
18296 TATC
1 TATC
18300 ACTACGAAGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (32 bp):
TATCGATACATAAGTGTTGTATCGATACAATA
Found at i:18363 original size:13 final size:13
Alignment explanation
Indices: 18345--18369 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18335 ATTGCTCAAA
18345 TGTATCGATACAT
1 TGTATCGATACAT
18358 TGTATCGATACA
1 TGTATCGATACA
18370 CTGATCATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:18367 original size:34 final size:33
Alignment explanation
Indices: 18324--18390 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 33
18314 GCCAAGAAAA
* *
18324 TGTATCGATACATTGCTCAAATGTATCGATACAT
1 TGTATCGATACACTGATC-AATGTATCGATACAT
*
18358 TGTATCGATACACTGATCATTGTATCGATACAT
1 TGTATCGATACACTGATCAATGTATCGATACAT
18391 GCAGGCAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 14 0.47
34 16 0.53
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (33 bp):
TGTATCGATACACTGATCAATGTATCGATACAT
Found at i:18434 original size:52 final size:52
Alignment explanation
Indices: 18360--18506 Score: 224
Period size: 52 Copynumber: 2.8 Consensus size: 52
18350 CGATACATTG
* *
18360 TATCGATACACTGAT-CATTGTATCGATACATGCAGGCAAATTTGCCCAGATA
1 TATCGATACACT-ATGAAATGTATCGATACATGCAGGCAAATTTGCCCAGATA
* * *
18412 TATCGATACACTATGAAATGTATCAATACATACAGGCAAATTTGCCCAGATG
1 TATCGATACACTATGAAATGTATCGATACATGCAGGCAAATTTGCCCAGATA
*
18464 TATCGATACACTATGAAATGTATCGATACATGTAGGCAAATTT
1 TATCGATACACTATGAAATGTATCGATACATGCAGGCAAATTT
18507 TCATATTTCG
Statistics
Matches: 86, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
51 2 0.02
52 84 0.98
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.29
Consensus pattern (52 bp):
TATCGATACACTATGAAATGTATCGATACATGCAGGCAAATTTGCCCAGATA
Found at i:23610 original size:13 final size:13
Alignment explanation
Indices: 23592--23619 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
23582 ATACAAAGAT
23592 CAATGTATCGATA
1 CAATGTATCGATA
23605 CAATGTATCGATA
1 CAATGTATCGATA
23618 CA
1 CA
23620 TTTGAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:23682 original size:13 final size:13
Alignment explanation
Indices: 23664--23747 Score: 60
Period size: 13 Copynumber: 5.5 Consensus size: 13
23654 AGCTTCATAG
23664 CGATACATTGTAT
1 CGATACATTGTAT
23677 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
23696 CGATACATTGTAT
1 CGATACATTGTAT
23709 CGATACAACACTTATGTAT
1 CGAT---ACA--T-TGTAT
23728 CGATACATTGTAT
1 CGATACATTGTAT
23741 CGATACA
1 CGATACA
23748 AATCATTGAA
Statistics
Matches: 59, Mismatches: 0, Indels: 24
0.71 0.00 0.29
Matches are distributed among these distances:
13 26 0.44
14 1 0.02
15 2 0.03
16 8 0.14
17 2 0.03
18 1 0.02
19 19 0.32
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:23696 original size:19 final size:18
Alignment explanation
Indices: 23672--23734 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
23662 AGCGATACAT
23672 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
23691 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
23704 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
23723 TGTATCGATACA
1 TGTATCGATACA
23735 TTGTATCGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
16 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:23705 original size:32 final size:32
Alignment explanation
Indices: 23664--23749 Score: 163
Period size: 32 Copynumber: 2.7 Consensus size: 32
23654 AGCTTCATAG
23664 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
23696 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
23728 CGATACATTGTATCGATACAAA
1 CGATACATTGTATCGATACAAA
23750 TCATTGAAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:24970 original size:13 final size:13
Alignment explanation
Indices: 24952--24976 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24942 ATTTTGCTTA
24952 GTATCGATACATT
1 GTATCGATACATT
24965 GTATCGATACAT
1 GTATCGATACAT
24977 AAAACTGACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:25031 original size:24 final size:24
Alignment explanation
Indices: 25004--25049 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
24994 AATCTCATTT
*
25004 TCACTGTTCATCACTATTCATGTA
1 TCACTATTCATCACTATTCATGTA
* *
25028 TCACTATTCATTACTGTTCATG
1 TCACTATTCATCACTATTCATG
25050 CATCGATACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.09, T:0.43
Consensus pattern (24 bp):
TCACTATTCATCACTATTCATGTA
Done.